Plants modified with mini-chromosomes

ABSTRACT

The invention is generally related to methods of generating plants transformed with novel autonomous mini-chromosomes. Mini-chromosomes with novel compositions and structures are used to transform plants cells which are in turn used to generate the plant. Methods for generating the plant include methods for delivering the mini-chromosome into plant cell to transform the cell, methods for selecting the transformed cell, and methods for isolating plants transformed with the mini-chromosome. Plants generated in the present invention contain novel genes introduced into their genome by integration into existing chromosomes.

RELATED APPLICATIONS

This application is a national phase filing of PCT Application No. PCT/US2005/006505, filed Feb. 23, 2005, which claims priority to U.S. Provisional Application No. 60/547,256 filed Feb. 23, 2004, which are incorporated by reference herein in its entirety.

BACKGROUND OF THE INVENTION

Two general approaches are used for introduction of new genetic information (“transformation”) into cells. One approach is to introduce the new genetic information as part of another DNA molecule, referred to as an “episomal vector,” or “mini-chromosome”, which can be maintained as an independent unit (an episome) apart from the host chromosomal DNA molecule(s). Episomal vectors contain all the necessary DNA sequence elements required for DNA replication and maintenance of the vector within the cell. Many episomal vectors are available for use in bacterial cells (for example, see Maniatis et al., “Molecular Cloning: a Laboratory Manual,” Cold Spring Harbor Laboratory, Cold Sprint Harbor, N.Y. 1982.). However, only a few episomal vectors that function in higher eukaryotic cells have been developed. Higher eukaryotic episomal vectors were primarily based on naturally occurring viruses. In higher plant systems gemini viruses are double-stranded DNA viruses that replicate through a double-stranded intermediate upon which an episomal vector could be based, although the gemini virus is limited to an approximately 800 bp insert. Although an episomal plant vector based on the Cauliflower Mosaic Virus has been developed, its capacity to carry new genetic information also is limited (Brisson et al., Nature, 310:511,1984).

The other general method of genetic transformation involves integration of introduced DNA sequences into the recipient cell's chromosomes, permitting the new information to be replicated and partitioned to the cell's progeny as a part of the natural chromosomes. The introduced DNA usually is broken and joined together in various combinations before it is integrated at random sites into the cell's chromosome (see, for example Wigler et al., Cell, 11:223, 1977). Common problems with this procedure are the rearrangement of introduced DNA sequences and unpredictable levels of expression due to the location of the transgene in the genome or so called “position effect variegation” (Shingo et al., Mol. Cell. Biol., 6:1787, 1986). Further, unlike episomal DNA, integrated DNA cannot normally be precisely removed. A more refined form of integrative transformation can be achieved by exploiting naturally occurring viruses that integrate into the host's chromosomes as part of their life cycle, such as retroviruses (see Chepko et al., Cell, 37:1053, 1984).

One common genetic transformation method used in higher plants is based on the transfer of bacterial DNA into plant chromosomes that occurs during infection by the phytopathogenic soil bacterium Agrobacterium (see Nester et al., Ann. Rev. Plant Phys., 35:387-413, 1984). By substituting genes of interest for the naturally transferred bacterial sequences (called T-DNA), investigators have been able to introduce new DNA into plant cells. However, even this more “refined” integrative transformation system is limited in three major ways. First, DNA sequences introduced into plant cells using the Agrobacterium T-DNA system are frequently rearranged (see Jones et al., Mol. Gen. Genet., 207:478, 1987). Second, the expression of the introduced DNA sequences varies between individual transformants (see Jones et al., EMBO J., 4:2411-2418, 1985). This variability is presumably caused by rearranged sequences and the influence of surrounding sequences in the plant chromosome (i.e., position effects), as well as methylation of the transgene. Finally, insertion of extra elements into the genome can disrupt the genes, promoters or other genetic elements necessary for normal plant growth and function.

Another widely used technique to genetically transform plants involves the use of micro-projectile bombardment. In this process, a nucleic acid containing the desired genetic elements to be introduced into the plant is deposited on or in small metallic particles, e.g., tungsten, platinum, or preferably gold, which are then delivered at a high velocity into the plant tissue or plant cells. However, similar problems arise as with Agrobacterium-mediated gene transfer, and as noted above expression of the inserted DNA can be unpredictable and insertion of extra elements into the genome can disrupt and adversely impact plant processes.

One attractive alternative to commonly used methods of transformation is the use of an artificial chromosome. Artificial chromosomes are man-made linear or circular DNA molecules constructed in part from cis-acting DNA sequence elements that provide replication and partitioning of the constructed chromosomes (see Murray et al., Nature, 305:189-193, 1983). Desired elements include: (1) origin of replication, which are the sites for initiation of DNA replication, (2) centromeres (site of kinetochore assembly and responsible for proper distribution of replicated chromosomes into daughter cells at mitosis or meiosis), and (3) if the chromosome is linear, telomeres (specialized DNA structures at the ends of linear chromosomes that function to stabilize the ends and facilitate the complete replication of the extreme termini of the DNA molecule). An additional desired element is a chromatin organizing sequence. It is well documented that centromere function is crucial for stable chromosomal inheritance in almost all eukaryotic organisms (reviewed in Nicklas 1988). The centromere accomplishes this by attaching, via centromere binding proteins, to the spindle fibers during mitosis and meiosis, thus ensuring proper gene segregation during cell divisions.

The essential chromosomal elements for construction of artificial chromosomes have been precisely characterized in lower eukaryotic species, and more recently in mouse and human. Autonomous replication sequences (ARSs) have been isolated from unicellular fungi, including Saccharomyces cerevisiae (brewer's yeast) and Schizosaccharomyces pombe (see Stinchcomb et al., 1979 and Hsiao et al., 1979). An ARS behaves like a origin of replication allowing DNA molecules that contain the ARS to be replicated in concert with the rest of the genome after introduction into the cell nuclei of these fungi. DNA molecules containing these sequences replicate, but in the absence of a centromere they are not partitioned into daughter cells in a controlled fashion that ensures efficient chromosome inheritance.

Artificial chromosomes have been constructed in yeast using the three cloned essential chromosomal elements (see Murray et al., Nature, 305:189-193, 1983). None of the essential components identified in unicellular organisms, however, function in higher eukaryotic systems. For example, a yeast centromere sequence will not confer stable inheritance upon vectors transformed into higher eukaryotes.

In contrast to the detailed studies done in yeast, less is known about the molecular structure of functional centromeric DNA of higher eukaryotes. Ultrastructural studies indicate that higher eukaryotic kinetochores, which are specialized complexes of proteins that form on the centromere during late prophase, are large structures (mammalian kinetochore plates are approximately 0.3 μm in diameter) which possess multiple microtubule attachment sites (reviewed in Rieder, 1982). It is therefore possible that the centromeric DNA regions of these organisms will be correspondingly large, although the minimal amount of DNA necessary for centromere function may be much smaller.

While the above studies have been useful in elucidating the structure and function of centromeres, it was not known whether information derived from lower eukaryotic or mammalian higher eukaryotic organisms would be applicable to plants. There exists a need for cloned centromeres from higher eukaryotic organisms, particularly plant organisms, which would represent a first step in production of artificial chromosomes. There further exists a need for plant cells, plants, seeds and progeny containing functional, stable, and autonomous artificial chromosomes capable of carrying a large number of different genes and genetic elements.

SUMMARY OF THE INVENTION

The invention provides for adchromosomal plants, described in further detail herein, comprising a mini-chromosome, wherein said mini-chromosome preferably has a transmission efficiency during mitotic division of at least 90%, for example, at least 95%. Additionally, these adchromosomal plants may comprise a mini-chromosome having a transmission efficiency during meiotic division of, e.g., at least 80%, at least 85%, at least 90% or at least 95%.

In one embodiment, the adchromosomal plants of the invention comprise a mini-chromosome that is 1000 kilobases or less in length. In exemplary embodiments, the adchromosomal plant comprises a mini-chromosome that is 600 kilobases or less in length or 500 kilobases or less in length.

In another embodiment, the mini-chromosome of any of the preceding adchromosomal plants of the invention comprises a site for site-specific recombination.

In an embodiment, the mini-chromosome of any of the preceding adchromosomal plants of the invention comprises a centromeric nucleic acid insert derived from a crop plant centromere. In an exemplary embodiment, the centromeric nucleic acid insert is derived from genomic DNA of a plant selected from the group consisting of Brassica, Nicotiana, Lycopersicum, Glycine or Zea species. In another exemplary embodiment, the centromeric nucleic acid insert is derived from genomic DNA of a plant selected from the group consisting of broccoli, canola, tobacco, tomato, soybean or corn.

In another embodiment, the invention provides for the mini-chromosome of any one of the preceding adchromosomal plants, further comprising a centromeric nucleic acid insert that comprises artificially synthesized repeated nucleotide sequences. These artificially synthesized repeated nucleotide sequences may be derived from natural centromere sequences, combinations or fragments of natural centromere sequences including a combination of repeats of different lengths, a combination of different sequences, a combination of both different repeat lengths and different sequences, a combination of repeats from two or more plant species, a combination of different artificially synthesized sequences or a combination of natural centromere sequence(s) and artificially synthesized sequence(s).

The invention also provides fora mini-chromosome of any of the preceding adchromosomal plants of the invention, wherein the mini-chromosome is derived from a donor clone or a centromere clone and has substitutions, deletions, insertions, duplications or arrangements of one or more nucleotides in the mini-chromosome compared to the nucleotide sequence of the donor clone or centromere clone. In one embodiment, the mini-chromosome is obtained by passage of the mini-chromosome through one or more hosts. In another embodiment, the mini-chromosome is obtained by passage of the mini-chromosome through two or more different hosts. The host may be selected from the group consisting of viruses, bacteria, yeasts, plants, prokaryotic organisms, or eukaryotic organisms.

The invention also provides for a mini-chromosome of any of the preceding adchromosomal plants of the invention, wherein the mini-chromosome comprises one or more exogenous nucleic acids. In further exemplary embodiments, the mini-chromosome comprises at least two or more, at least three or more, at least four or more, at least five or more or at least ten or more exogenous nucleic acids.

In one embodiment, at least one exogenous nucleic acid of any of the preceding mini-chromosomes of a plant is operably linked to a heterologous regulatory sequence functional in plant cells. The invention provides for exogenous nucleic acids linked to a plant regulatory sequence. The invention also provides for exogenous nucleic acids linked to a non-plant regulatory sequence, such as an inset or yeast regulatory sequence. Exemplary regulatory sequences comprise any one of SEQ ID NOS: 4 to 23 or a functional fragment or variant thereof.

In another embodiment, the mini-chromosome of any of the preceding adchromosomal plants comprises an exogenous nucleic acid that confers herbicide resistance, insect resistance, disease resistance, or stress resistance on the plant. The invention provides for mini-chromosomes comprising an exogenous nucleic acid that confers resistance to phosphinothricin or glyphosate herbicide. The invention also provides for mini-chromosomes comprising an exogenous nucleic acid that encodes a phosphinothricin acetyltransferase, glyphosate acetyltransferase or a mutant enolpyruvylshikimate phosphate (EPSP) synthase.

The invention also provides for the mini-chromosome of any of the preceding adchromosomal plants comprising an exogenous nucleic acid that encodes a Bacillus thuringiensis crystal toxin gene or Bacillus cereus toxin gene. The invention further provides for the mini-chromosome of any of the preceding adchromosomal plants comprising an exogenous nucleic acid that confers resistance to drought, heat, chilling, freezing, excessive moisture, ultraviolet light, ionizing radiation, toxins, pollution, mechanical stress or salt stress. The invention also provides for a mini-chromosome of any of the preceding adchromosomal plants that comprises an exogenous nucleic acid that confers resistance to a virus, bacteria, fungi or nematode.

In another embodiment, the mini-chromosome of any of the preceding adchromosomal plants comprises an exogenous nucleic acid conferring herbicide resistance, an exogenous nucleic acid conferring insect resistance, and at least one additional exogenous nucleic acid.

The invention provides for mini-chromosomes of any of the preceding adchromosomal plants comprising an exogenous nucleic acid selected from the group consisting of a nitrogen fixation gene, a plant stress-induced gene, a nutrient utilization gene, a gene that affects plant pigmentation, a gene that encodes an antisense or ribozyme molecule, a gene encoding a secretable antigen, a toxin gene, a receptor gene, a ligand gene, a seed storage gene, a hormone gene, an enzyme gene, an interleukin gene, a clotting factor gene, a cytosine gene, an antibody gene, a growth factor gene, a transcription factor gene, a transcriptional repressor gene, a DNA-binding protein gene, a recombination gene, a DNA replication gene, a programmed cell death gene, a kinase gene, a phosphatase gene, a G protein gene, a cyclin gene, a cell cycle control gene, a gene involved in transcription, a gene involved in translation, a gene involved in RNA processing, a gene involved in RNAi, an organellar gene, a intracellular trafficking gene, an integral membrane protein gene, a transporter gene, a membrane channel protein gene, a cell wall gene, a gene involved in protein processing, a gene involved in protein modification, a gene involved in protein degradation, a gene involved in metabolism, a gene involved in biosynthesis, a gene involved in assimilation of nitrogen or other elements or nutrients, a gene involved in controlling carbon flux, gene involved in respiration, a gene involved in photosynthesis, a gene involved in light sensing, a gene involved in organogenesis, a gene involved in embryogenesis, a gene involved in differentiation, a gene involved in meiotic drive, a gene involved in self incompatibility, a gene involved in development, a gene involved in nutrient, metabolite or mineral transport, a gene involved in nutrient, metabolite or mineral storage, a calcium-binding protein gene, or a lipid-binding protein gene.

The invention also provides for a mini-chromosome of any of the preceding adchromosomal plants comprising an exogenous enzyme gene selected from the group consisting of a gene that encodes an enzyme involved in metabolizing biochemical wastes for use in bioremediation, a gene that encodes an enzyme for modifying pathways that produce secondary plant metabolites, a gene that encodes an enzyme that produces a pharmaceutical, a gene that encodes an enzyme that improves changes the nutritional content of a plant, a gene that encodes an enzyme involved in vitamin synthesis, a gene that encodes an enzyme involved in carbohydrate, polysaccharide or starch synthesis, a gene that encodes an enzyme involved in mineral accumulation or availability, a gene that encodes a phytase, a gene that encodes an enzyme involved in fatty acid, fat or oil synthesis, a gene that encodes an enzyme involved in synthesis of chemicals or plastics, a gene that encodes an enzyme involved in synthesis of a fuel and a gene that encodes an enzyme involved in synthesis of a fragrance, a gene that encodes an enzyme involved in synthesis of a flavor, a gene that encodes an enzyme involved in synthesis of a pigment or dye, a gene that encodes an enzyme involved in synthesis of a hydrocarbon, a gene that encodes an enzyme involved in synthesis of a structural or fibrous compound, a gene that encodes an enzyme involved in synthesis of a food additive, a gene that encodes an enzyme involved in synthesis of a chemical insecticide, a gene that encodes an enzyme involved in synthesis of an insect repellent, or a gene controlling carbon flux in a plant.

In an embodiment of the invention, the mini-chromosomes of any one of the preceding adchromosomal plants comprise n copies of a repeated nucleotide sequence, wherein n is less than 1000. In other exemplary embodiments, the mini-chromosomes of the plants comprise n copies of a repeated nucleotide sequence, wherein n is at least 5, wherein n is at least 15, or wherein n is at least 50.

In another embodiment of the invention, the mini-chromosomes of any of the preceding adchromosomal plants comprise a telomere.

The invention also provides embodiments wherein the mini-chromosome of any of the preceding adchromosomal plants is circular.

In one embodiment of the invention, any of the preceding adchromosomal plants are a monocotyledon. In another embodiment of the invention, any of the preceding adchromosomal plants are a dicotyledone. The invention also provides that the adchromosomal plants of the invention are, e.g., crop plants, cereal plants, vegetable crops, field crops, fruit and vine crops, wood or fiber crops or ornamental plants. The invention also provides exemplary adchromosomal plants that are Brassica, Nicotiana, Lycopersicum, Glycine or Zea species.

Another embodiment of the invention is a part of any of the preceding adchromosomal plants. Exemplary plant parts of the invention include a pod, root, cutting, tuber, stem, stalk, fruit, berry, nut, flower, leaf, bark, wood, epidermis, vascular tissue, organ, protoplast, crown, callus culture, petiole, petal, sepal, stamen, stigma, style, bud, meristem, cambium, cortex, pith, sheath, silk or embryo. Other exemplary plant parts are a meiocyte or gamete or ovule or pollen or endosperm of any of the preceding adchromosomal plants. Other exemplary plant parts are a seed, embryo or propagule of any of the preceding adchromosomal plants.

An embodiment of the invention is a progeny of any of the preceding adchromosomal plants of the invention. These progeny of the invention may be the result of self-breeding, cross-breeding, apomyxis or clonal propagation. In exemplary embodiments, the invention also provides for progeny that comprise a mini-chromosome that is descended from a parental mini-chromosome that contained a centromere less than 150 kilobases in length, less than 100 kilobases in length or less than 50 kilobases in length.

In another aspect, the invention provides for methods of making a mini-chromosome for use in any of the preceding adchromosomal plants of the invention. These methods comprise identifying a centromere nucleotide sequence in a genomic DNA library using a multiplicity of diverse probes, and constructing a mini-chromosome comprising the centromere nucleotide sequence. These methods may further comprise determining hybridization scores for hybridization of the multiplicity of diverse probes to genomic clones within the genomic nucleic acid library, determining a classification for genomic clones within the genomic nucleic acid library according to the hybridization scores for at least two of the diverse probes, and selecting one or more genomic clones within one or more classifications for constructing the mini-chromosome.

In exemplary embodiments, the step of determining a classification for genomic clones within the genomic nucleic acid library may utilize the hybridization scores for at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 or more different probes. A classification may comprise a pattern of high, medium or low hybridization scores to various probes.

Exemplary embodiments of probes useful in this method include a probe that hybridizes to the centromere region of a chromosome, a probe that hybridizes to satellite repeat DNA, a probe that hybridizes to retroelement DNA, a probe that hybridizes to portions of genomic DNA that are heavily methylated, a probe that hybridizes to arrays of tandem repeats in genomic DNA, a probe that hybridizes to telomere DNA or a probe that hybridizes to a pseudogene. Other exemplary probes include, a probe that hybridizes to ribosomal DNA, a probe that hybridizes to mitochondrial DNA, or a probe that hybridizes to chloroplast DNA, for which preferably a classification comprises a low hybridization score for hybridization to said probe.

Another aspect of the invention provides for methods of making any one of the preceding adchromosomal plants comprising delivering a mini-chromosome to a plant cell using a biolistic method, wherein a particle suitable for use in biolistic method is delivered in a liquid with the mini-chromosome, and regenerating a plant from the plant cell. The liquid may further comprise a divalent ion and a di- or poly-amine. In exemplary embodiments, the liquid comprises water, CaCl₂, and spermidine, and the particles are gold particles. Suitable alternatives to spermidine are, e.g., spermine or other aliphatic or conjugated di- or poly-amines such as 1,5-diaminopentane, 1,6-diaminohexane, 1,7-diaminoheptane, 1,8-diaminooctane, histamine or related molecules.

A further aspect of the invention provides for methods of making any of the preceding adchromosomal plant comprising co-delivering to a plant cell a mini-chromosome and a nucleic acid encoding a growth inducing gene, wherein said nucleic acid is not part of the mini-chromosome, and regenerating a plant from the plant cell. The invention further provides for methods comprising co-delivering a nucleic acid encoding a growth inducing gene is not expressed or alternatively is not present in the regenerated plant. The invention also provides for methods wherein the co-delivered nucleic acid encodes a growth inducing gene expressed during regeneration. The growth inducing gene may a plant growth regulator gene, an organogenesis-promoting gene, an embryogenesis-promoting gene or regeneration-promoting gene, such as Agrobacterium tumefaciens isopentenyl transferase gene, Agrobacterium rhizogenes isopentenyl transferase gene, Agrobacterium tumefaciens indole-3-acetamide hydrolase (IAAH) gene or Agrobacterium tumefaciens tryptophan-2-monooxygenase (IAAM) gene.

Another aspect of the invention provides for methods of using any of the preceding adchromosomal plants for a food product, a pharmaceutical product or chemical product, according to which a suitable exogenous nucleic acid is expressed in adchromosomal plants or plant cells and the plant or plant cells are grown. The plant may secrete the product into its growth environment or the product may be contained within the plant, in which case the plant is harvested and desirable products are extracted.

Thus, the invention contemplates methods of using any of the preceding adchromosomal plants to produce a modified food product, for example, by growing a plant that expresses a exogenous nucleic acid that alters the nutritional content of the plant, and harvesting or processing the corn plant.

The invention also contemplates methods of using any of the preceding adchromosomal plants to produce a recombinant protein, by growing a plant comprising a mini-chromosome that comprises an exogenous nucleic acid encoding the recombinant protein. Optionally the plant is harvested and the desired recombinant protein is isolated from the plant. Exemplary recombinant proteins include pharmaceutical proteins or industrial enzymes.

The invention also contemplates methods of using any of the preceding adchromosomal plants to produce a recombinant protein, by growing a plant comprising a mini-chromosome that comprises an exogenous nucleic acid encoding an enzyme involved in synthesis of the chemical product. Optionally the plant is harvested and the desired chemical product is isolated from the plant. Exemplary chemical products include pharmaceutical products.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is an example of a mini-chromosome vector in the present invention containing 2 genes;

FIG. 2 is another example of a mini-chromosome vector in the present invention containing 4 genes;

FIG. 3 is a mini-chromosome from which all bacterial sequences have been removed. In this embodiment, bacterial sequence present between or among the plant-expressed genes or other mini-chromosome sequences would be excised prior to removal of the remaining bacterial sequences, by cutting the mini-chromosome with endonuclease #1, and re-ligating the structure such that the antibiotic-resistance gene #1 has been lost.

FIG. 4 shows various structural configurations by which mini-chromosome elements can be oriented with respect to each other.

FIG. 5 shows the alignment of Brassica consensus centromere satellite repeats, BB5R4-1 (SEQ ID NO:2), BB5R4-1 (SEQ ID NO:51), and BB280R2-3 (SEQ ID NO:52).

FIG. 6 shows the alignment of Glycine max (soybean) consensus centromere satellite repeats, CrGM1 (SEQ ID NO:25), CrGm2 (SEQ ID NO:26), and SB12MC (SEQ ID NO:24).

DETAILED DESCRIPTION OF THE INVENTION

While this invention is susceptible of embodiment in many different forms, there is shown in the drawings, and will be described herein in detail, specific embodiments thereof with the understanding that the present disclosure is to be considered as an exemplification of the principles of the invention and is not intended to limit the invention to the specific embodiments illustrated.

The invention is based on the production of modified plants, containing functional, stable, autonomous mini-chromosomes. Such mini-chromosomes have been shown herein to be meiotically transmitted to progeny.

One aspect of the invention is related to plants containing functional, stable, autonomous mini-chromosomes, preferably carrying one or more nucleic acids exogenous to the cell. Such plants carrying mini-chromosomes are contrasted to transgenic plants whose genome has been altered by chromosomal integration of an exogenous nucleic acid. Preferably, expression of the exogenous nucleic acid, either constitutively or in response to a signal which may be a challenge or a stimulus, results in an altered phenotype of the plant.

The invention provides for mini-chromosomes comprising at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 250, 500, 1000 or more exogenous nucleic acids.

The invention contemplates that any plants, including but not limited to monocots, dicots, gymnosperm, field crops, vegetable crops, fruit and vine crops, or any specific plants named herein, may be modified by carrying autonomous mini-chromosomes as described herein. A related aspect of the invention is plant parts or plant tissues, including pollen, silk, endosperm, ovule, seed, embryo, pods, roots, cuttings, tubers, stems, stalks, fruit, berries, nuts, flowers, leaves, bark, whole plant, plant cell, plant organ, protoplast, cell culture, or any group of plant cells organized into a structural and functional unit, any cells of which carry mini-chromosomes.

A related aspect of the invention is adchromosomal plant parts or plant tissues, including pollen, silk, endosperm, ovule, seed, embryo, pods, roots, cuttings, tubers, stems, stalks, crown, callus culture, petiole, petal, sepal, stamen, stigma, style, bud, fruit, berries, nuts, flowers, leaves, bark, wood, whole plant, plant cell, plant organ, protoplast, cell culture, or any group of plant cells organized into a structural and functional unit. In one preferred embodiment, the exogenous nucleic acid is primarily expressed in a specific location or tissue of a plant, for example, epidermis, vascular tissue, meristem, cambium, cortex, pith, leaf, sheath, flower, root or seed. Tissue-specific expression can be accomplished with, for example, localized presence of the mini-chromosome, selective maintenance of the mini-chromosome, or with promoters that drive tissue-specific expression.

Another related aspect of the invention is meiocytes, pollen, ovules, endosperm, seed, somatic embryos, apomyctic embryos, embryos derived from fertilization, vegetative propagules and progeny of the originally adchromosomal plant and of its filial generations that retain the functional, stable, autonomous mini-chromosome. Such progeny include clonally propagated plants, embryos and plant parts as well as filial progeny from self- and cross-breeding, and from apomyxis.

Preferably the mini-chromosome is transmitted to subsequent generations of viable daughter cells during mitotic cell division with a transmission efficiency of at least 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%. More preferably, the mini-chromosome is transmitted to viable gametes during meiotic cell division with a transmission efficiency of at least 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% when more than one copy of the mini-chromosome is present in the gamete mother cells of the plant. Preferably, the mini-chromosome is transmitted to viable gametes during meiotic cell division with a transmission frequency of at least 20%, 30%, 40%, 45%, 46%, 47%, 48%, or 49% when one copy of the mini-chromosome is present in the gamete mother cells of the plant. For production of seeds via sexual reproduction or by apomyxis the mini-chromosome is preferably transferred into at least 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% of viable embryos when cells of the plant contain more than one copy of the mini-chromosome. For production of seeds via sexual reproduction or by apomyxis from plants with one mini-chromosome per cell, the mini-chromosome is preferably transferred into at least 20%, 30%, 40%, 45%, 46%, 47%, 48%, or 49% of viable embryos.

Preferably, a mini-chromosome that comprises an exogenous selectable trait or exogenous selectable marker can be employed to increase the frequency in subsequent generations of adchromosomal cells, tissues, gametes, embryos, endosperm, seeds, plants or progeny. More preferably, the frequency of transmission of mini-chromosomes into viable cells, tissues, gametes, embryos, endosperm, seeds, plants or progeny can be at least 95%, 96%, 97%, 98%, 99% or 99.5% after mitosis or meiosis by applying a selection that favors the survival of adchromosomal cells, tissues, gametes, embryos, endosperm, seeds, plants or progeny over such cells, tissues, gametes, embryos, endosperm, seeds, plants or progeny lacking the mini-chromosome.

Transmission efficiency may be measured as the percentage of progeny cells or plants that carry the mini-chromosome as measured by one of several assays taught herein including detection of reporter gene fluorescence, PCR detection of a sequence that is carried by the mini-chromosome, RT-PCR detection of a gene transcript for a gene carried on the mini-chromosome, Western analysis of a protein produced by a gene carried on the mini-chromosome, Southern analysis of the DNA (either in total or a portion thereof) carried by the mini-chromosome, fluorescence in situ hybridization (FISH) or in situ localization by repressor binding, to name a few. Any assay used to detect the presence of the mini-chromosome (or a portion of the mini-chromosome) may be used to measure the efficiency of a parental cell or plant transmits the mini-chromosome to its progeny. Efficient transmission as measured by some benchmark percentage should indicate the degree to which the mini-chromosome is stable through the mitotic and meiotic cycles.

Plants of the invention may also contain chromosomally integrated exogenous nucleic acid in addition to the autonomous mini-chromosomes. The adchromosomal plants or plant parts, including plant tissues of the invention may include plants that have chromosomal integration of some portion of the mini-chromosome in some or all cells the plant. The plant, including plant tissue or plant cell is still characterized as adchromosomal despite the occurrence of some chromosomal integration. In one aspect of the invention, the autonomous mini-chromosome can be isolated from integrated exogenous nucleic acid by crossing the adchromosomal plant containing the integrated exogenous nucleic acid with plants producing some gametes lacking the integrated exogenous nucleic acid and subsequently isolating offspring of the cross, or subsequent crosses, that are adchromosomal but lack the integrated exogenous nucleic acid. This independent segregation of the mini-chromosome is one measure of the autonomous nature of the mini-chromosome.

Another aspect of the invention relates to methods for producing and isolating such adchromosomal plants containing functional, stable, autonomous mini-chromosomes.

In one embodiment, the invention contemplates improved methods for isolating native centromere sequences. In another embodiment, the invention contemplates methods for generating variants of native or artificial centromere sequences by passage through bacterial or plant or other host cells.

In a further embodiment, the invention contemplates methods for delivering the mini-chromosome into plant cells or tissues to transform the cells or tissues.

In yet another embodiment, the invention contemplates improved methods for regenerating plants, including methods for co-delivery of growth inducing genes with mini-chromosomes. The growth delivery genes include Agrobacterium tumefaciens or A. rhizogenes isopentenyl transferase (IPT) genes involved in cytokinin biosynthesis, plant isopentenyl transferase (IPT) genes involved in cytokinin biosynthesis (from any plant), Agrobacterium tumefaciens IAAH, IAAM genes involved in auxin biosynthesis (indole-3-acetamide hydrolase and tryptophan-2-monooxygenase, respectively), Agrobacterium rhizogenes rolA, rolB and rolC genes involved in root formation, Agrobacterium tumefaciens Aux1, Aux2 genes involved in auxin biosynthesis (indole-3-acetamide hydrolase or tryptophan-2-monooxygenase genes), Arabidopsis thaliana leafy cotyledon genes (e.g. Lec1, Lec2) promoting embryogenesis and shoot formation (see Stone et al., Proc. Natl. Acad. Sci. USA 98: 11806-11811), Arabidopsis thaliana ESR1 gene involved in shoot formation (see Banno et al., Plant Cell 13: 2609-2618), Arabidopsis thaliana PGA6/WUSCHEL gene involved in embryogenesis (see Zuo et al., Plant J. 30: 349-359).

In yet a further embodiment, the invention contemplates methods for selecting modified plant cells or plant parts containing mini-chromosomes for regeneration. Such methods include assays for identifying adchromosomal plants or cells by determining that mini-chromosomes within the modified plant cell or plant are functional, stable, and autonomous. Exemplary assays for assessing mini-chromosome performance include lineage-based inheritance assays, use of chromosome loss agents to demonstrate autonomy, global mitotic mini-chromosome inheritance assays (sectoring assays) with or without the use of agents inducing chromosomal loss, assays measuring expression levels of marker genes in the mini-chromosome over time and space in a plant, physical assays for separation of autonomous mini-chromosomes from endogenous nuclear chromosomes of plants, molecular assays demonstrating conserved mini-chromosome structure, such as PCR, Southern blots, mini-chromosome rescue, cloning and characterization of mini-chromosome sequences present in the plant, cytological assays detecting mini-chromosome presence in the cell's genome (e.g. FISH) and meiotic mini-chromosome inheritance assays, which measure the levels of mini-chromosome inheritance into a subsequent generation of plants via meiosis and gametes, embryos, endosperm or seeds.

The invention also contemplates novel methods of screening for adchromosomal plant cells that involve use of relatively low, sub-killing concentrations of selection agent (e.g. sub-killing antibiotic concentrations), and also involve use of a screenable marker (e.g., a visible marker gene) to identify clusters of modified cells carrying the screenable marker, after which these screenable cells are manipulated to homogeneity. Another aspect of the present invention is related to methods of making and compositions of non-plant promoters for expressing genes in plants.

The invention further provides isolated promoter nucleic acid sequences comprising any one of SEQ ID NOS: 4 to 23, or fragments or variants thereof that retain expression-promoting activity. Mini-chromosomes comprising non-plant promoter sequences such as these that are operably linked to plant-expressed genes (e.g., genes that confer a different phenotype on plants), are contemplated as are plants comprising such mini-chromosomes.

Another aspect is related to methods for using exonuclease to enrich for circular mini-chromosome DNA in genomic DNA preparations.

Another aspect of the invention relates to methods for using such adchromosomal plants containing a mini-chromosome for producing food products, pharmaceutical products and chemical products by appropriate expression of exogenous nucleic acid(s) contained within the mini-chromosome(s).

It has also been shown herein that mini-chromosomes containing centromeres from one plant species, when inserted into plant cells of a different species or even a different genus or family, can be stable, functional and autonomous. For example, as shown herein, a broccoli centromere (B. oleraceae) is functional in a canola (B. napus) plant. Similarly, a tomato (Lycopersicum) centromere is functional in a tobacco (Nicotiana) plant. A soybean (G. max) centromere is functional in a broccoli (B. oleraceae) and tobacco plant. Tobacco and tomato are in the same family of Solanaceae plants. Soybean is in the Leguminoseae family and broccoli is in the Brassicaceae family. Thus, another aspect of the invention is an adchromosomal plant comprising a functional, stable, autonomous mini-chromosome that contains centromere sequence derived from a different taxonomic plant species, or derived from a different taxonomic plant species, genus, family, order or class.

Yet another aspect of the invention provides novel autonomous mini-chromosomes with novel compositions and structures which are used to transform plant cells which are in turn used to generate a plant (or multiple plants). Exemplary mini-chromosomes of the invention are contemplated to be of a size 2000 kb or less in length. Other exemplary sizes of mini-chromosomes include less than or equal to, e.g., 1500 kb, 1000 kb, 900 kb, 800 kb, 700 kb, 600 kb, 500 kb, 450 kb, 400 kb, 350 kb, 300 kb, 250 kb, 200 kb, 150 kb, 100 kb, 80 kb, 60 kb, or 40 kb in length.

In a related aspect, novel centromere compositions as characterized by sequence content, size or other parameters are provided. Preferably, the minimal size of centromeric sequence is utilized in mini-chromosome construction. Exemplary sizes include a centromeric nucleic acid insert derived from a portion of plant genomic DNA, that is less than or equal to 1000 kb, 900 kb, 800 kb, 700 kb, 600 kb, 500 kb, 400 kb, 300 kb, 200 kb, 150 kb, 100 kb, 95 kb, 90 kb, 85 kb, 80 kb, 75 kb, 70 kb, 65 kb, 60 kb, 55 kb, 50 kb, 45 kb, 40 kb, 35 kb, 30 kb, 25 kb, 20 kb, 15 kb, 10 kb, 5 kb, or 2 kb in length. For example, rescued functional variant soybean centromeric sequences have been shown to be less than 30 kb in size. Another related aspect is the novel structure of the mini-chromosome, particularly structures lacking bacterial sequences, e.g, required for bacterial propagation.

In exemplary embodiments the invention contemplates mini-chromosomes or other vectors comprising a repeated nucleotide sequence derived from a Brassica plant and adchromosomal plants or parts containing these mini-chromosomes. Exemplary repeated nucleotide sequences include (1) SEQ ID NO:1, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO: 51 or SEQ ID NO: 52, or fragments or variants thereof, (2) combinations of any of these Brassica sequences or a fragment or variant thereof with another Brassica-derived centromeric nucleotide sequence, (3) combinations of any of these Brassica sequences or a fragment or variant thereof with a centromeric nucleotide sequence derived from a different plant species, and (4) combinations of any of the above with artificially synthesized centromeric nucleotide sequences.

In exemplary embodiments the invention also contemplates mini-chromosomes or other vectors comprising a repeated nucleotide sequence derived from a Glycine max plant and adchromosomal plants or parts containing these mini-chromosomes. Exemplary repeated nucleotide sequences include (1) SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO:26, or fragments or variants thereof, (2) combinations of any of these soybean sequences or a fragment or variant thereof with another soybean-derived centromeric nucleotide sequence, (3) combinations of any of these soybean sequences or a fragment or variant thereof with a centromeric nucleotide sequence derived from a different plant species, and (4) combinations of any of the above with artificially synthesized centromeric nucleotide sequences.

In exemplary embodiments, the invention also contemplates mini-chromosomes or other vectors comprising fragments or variants of the genomic DNA inserts of the BAC clones [identified as BB5, SB6, TB99, ZB19, or ZB113] deposited on Feb. 23, 2005 with the American Type Culture Collection (ATCC), P.O. Box 1549 Manassas, Va. 20108, USA, under Accession Nos. PTA-6601, PTA-6602, PTA-6603, PTA-6604 and PTA-6605, respectively, or naturally occurring descendants thereof, that retain the ability to segregate during mitotic or meiotic division as described herein, as well as adchromosomal plants or parts containing these mini-chromosomes. Other exemplary embodiments include fragments or variants of the genomic DNA inserts of any of the BAC clones identified herein, or descendants thereof, and fragments or variants of the centromeric nucleic acid inserts of any of the vectors or mini-chromosomes identified herein.

In other exemplary embodiments, the invention contemplates mini-chromosomes or other vectors comprising centromeric nucleotide sequence that when hybridized to 1, 2, 3, 4, 5, 6, 7, 8 or more of the probes described in the examples herein, under hybridization conditions described herein, e.g. low, medium or high stringency, provides relative hybridization scores as described in the examples herein. Preferably the probes for which relative hybridization scores are described herein as 5/10 or greater are used, and a hybridization signal greater than background for one or more of these probes is used to select clones. Adchromosomal plants or parts containing such mini-chromosomes are contemplated.

The advantages of the present invention include: provision of an autonomous, independent genetic linkage group for accelerating breeding; lack of disruption of host genome; multiple gene “stacking” of large numbers of genes with a potentially unlimited payload; uniformity of genetic composition exogenous DNA sequences in plant cells and plants containing autonomous mini-chromosomes; defined genetic context for predictable gene expression; higher frequency occurrence and recovery of plant cells and plants containing stably maintained exogenous DNA due to elimination of inefficient integration step; and the ability to eliminate mini-chromosomes in any tissues.

I. Composition of Mini-Chromosomes and Mini-Chromosome Construction

The mini-chromosome vector of the present invention may contain a variety of elements, including (1) sequences that function as plant centromeres, (2) one or more exogenous nucleic acids, including, for example, plant-expressed genes, (3) sequences that function as an origin of replication, which may be included in the region that functions as plant centromere, (4) optionally, a bacterial plasmid backbone for propagation of the plasmid in bacteria, (5) optionally, sequences that function as plant telomeres, (6) optionally, additional “stuffer DNA” sequences that serve to separate the various components on the mini-chromosome from each other, (7) optionally “buffer” sequences such as MARs or SARs, (8) optionally marker sequences of any origin, including but not limited to plant and bacterial origin, (9) optionally, sequences that serve as recombination sites, and (10) “chromatin packaging sequences” such as cohesion and condensing binding sites.

The mini-chromosomes of the present invention may be constructed to include various components which are novel, which include, but are not limited to, the centromere comprising novel repeating centromeric sequences, and the promoters, particularly promoters derived from non-plant species, as described in further detail below.

The mini-chromosomes of the present invention may be constructed to include various components which are novel, which include, but are not limited to, the centromere comprising novel repeating centromeric sequences, and the promoters, particularly promoters derived from non-plant species, as described in further detail below.

Novel Centromere Compositions

The centromere in the mini-chromosome of the present invention may comprise novel repeating centromeric sequences. An example of the mini-chromosome in the present invention is the Brassica BB5R4-1 mini-chromosome. The sequences set out as SEQ ID NOS:1 to 3 are relevant to the BB5R4-mini-chromosomes. The centromere of the BB5R4-1 mini-chromosome is 50 kb of Brassica centromere DNA as determined by CHEF gel analysis. To determine the sequence composition of the centromere, the mini-chromosome was randomly sheared and small fragments were cloned for sequencing, from which 11,010 bases of sequence were obtained from the centromere insert, a 0.17x coverage of the centromere. Of this sequence 9,533 bases were composed of centromere satellite repeat, the consensus of which is shown in SEQ ID NO:2. The satellite repeat was found to be 180+/−2 bp long. The remaining 1,477 bases of mini-chromosome sequence covered a unique sequence set out as SEQ ID NO:3. This sequence is considered a sampling of the centromere content of BB5R4-1.

Additional sequence analysis of another sampling of the Brassica centromere content of BB5R4-1 analyzing 7 contigs (1,175, 176, 177, 180, 184) that contain 118 canrep repeats from BB5R4-0.1 with repeat lengths of 113×176 bp, 1×175 bp and 4×174 bp generated the consensus sequence set out in SEQ ID NO: 51. A consensus sequence was also built from 135 tandem repeats obtained from another mini-chromosome, BB280R2-3; from the largest contig (33703 kb) spanning a total of 23782 bp. The repeat lengths are: 125×176 bp, 4×182 bp, 4×175 bp and 2×177 bp and this sequence is set out as SEQ ID NO: 52. An alignment of SEQ ID NOS: 2, 51 and 52 is set out in FIG. 5.

In another example, individual satellite repeats from soybean BAC clone SB12R2-3 (SEQ ID NO: 24) showed an average of 91.3% (s.d.=11.3%) identity to each other, with specific regions showing significantly higher and lower levels of variability. Comparing the satellite repeat consensus from SB12R2-3 to that obtained from randomly sampled soybean satellite sequences ChrGm1 (SEQ ID NO: 25) and ChrGm2 (SEQ ID NO: 26), see U.S. Patent Application 20030124561: Plant centromere compositions) identified several bases that differed significantly (χ² test, P<0.05). The SB12MC satellite repeats showed an average length of 91.07±0.40 bp, similar to the ChrGm2 91-base consensus and differing from the ChrGm1 92-base consensus. An alignment of the of consensus centromere satellite repeats is set out in FIG. 6.

Exemplary embodiments of centromere nucleic acid sequences according to the present invention include fragments or variants of the genomic DNA inserts of the BAC clones [identified as BB5, SB6, TB99, ZB19, or ZB113 deposited on Feb. 23, 2005 with the American Type Culture Collection (ATCC), P.O. Box 1549 Manassas, Va. 20108, USA, under Accession Nos. PTA-6601, PTA-6602, PTA-6603, PTA-6604 and PTA-6605, respectively, that retain the ability to segregate during mitotic or meiotic division as described herein. Variants of such sequences include artificially produced modifications as described herein and modifications produced via passaging through one or more bacterial, plant or other host cells as described herein.

Vectors comprising one, two, three, four, five, six, seven, eight, nine, ten, 15 or 20 or more of the elements contained in any of the exemplary vectors described in the examples below are also contemplated.

The invention specifically contemplates the alternative use of fragments or variants (mutants) of any of the nucleic acids described herein that retain the desired activity, including nucleic acids that function as centromeres, nucleic acids that function as promoters or other regulatory control sequences, or exogenous nucleic acids. Variants may have one or more additions, substitutions or deletions of nucleotides within the original nucleotide sequence. Variants include nucleic acid sequences that are at least 50%, 55%, 60, 65, 70, 75, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identical to the original nucleic acid sequence. Variants also include nucleic acid sequences that hybridize under low, medium, high or very high stringency conditions to the original nucleic acid sequence. Similarly, the specification also contemplates the alternative use of fragments or variants of any of the polypeptides described herein.

The comparison of sequences and determination of percent identity between two nucleotide sequences can be accomplished using a mathematical algorithm. In a preferred embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (1970) J. Mol. Biol. 48:444-453 algorithm which has been incorporated into the GAP program in the GCG software package, using either a Blossum 62 matrix or a PAM250 matrix. Preferably parameters are set so as to maximize the percent identity.

As used herein, the term “hybridizes under low stringency, medium stringency, and high stringency conditions” describes conditions for hybridization and washing. Guidance for performing hybridization reactions can be found in Current Protocols in Molecular Biology (1989) John Wiley & Sons, N.Y., 6.3.1-6.3.6, which is incorporated by reference. Aqueous and non-aqueous methods are described in that reference and either can be used. Specific hybridization conditions referred to herein are as follows: 1) low stringency hybridization conditions in 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by two washes in 0.5×SSC, 0.1% SDS, at least at 50° C.; 2) medium stringency hybridization conditions in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 55° C.; 3) high stringency hybridization conditions in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 65° C.

Mini-Chromosome Sequence Content and Structure

Plant-expressed genes from non-plant sources may be modified to accommodate plant codon usage, to insert preferred motifs near the translation initiation ATG codon, to remove sequences recognized in plants as 5′ or 3′ splice sites, or to better reflect plant GC/AT content. Plant genes typically have a GC content of more than 35%, and coding sequences which are rich in A and T nucleotides can be problematic. For example, ATTTA motifs may destabilize mRNA; plant polyadenylation signals such as AATAAA at inappropriate positions within the message may cause premature truncation of transcription; and monocotyledons may recognize AT-rich sequences as splice sites.

Each exogenous nucleic acid or plant-expressed gene may include a promoter, a coding region and a terminator sequence, which may be separated from each other by restriction endonuclease sites or recombination sites or both. Genes may also include introns, which may be present in any number and at any position within the transcribed portion of the gene, including the 5′ untranslated sequence, the coding region and the 3′ untranslated sequence. Introns may be natural plant introns derived from any plant, or artificial introns based on the splice site consensus that has been defined for plant species. Some intron sequences have been shown to enhance expression in plants. Optionally the exogenous nucleic acid may include a plant transcriptional terminator, non-translated leader sequences derived from viruses that enhance expression, a minimal promoter, or a signal sequence controlling the targeting of gene products to plant compartments or organelles.

The coding regions of the genes can encode any protein, including but not limited to visible marker genes (for example, fluorescent protein genes, other genes conferring a visible phenotype to the plant) or other screenable or selectable marker genes (for example, conferring resistance to antibiotics, herbicides or other toxic compounds or encoding a protein that confers a growth advantage to the cell expressing the protein) or genes which confer some commercial or agronomic value to the adchromosomal plant. Multiple genes can be placed on the same mini-chromosome vector, limited only by the number of restriction endonuclease sites or site-specific recombination sites present in the vector. The genes may be separated from each other by restriction endonuclease sites, homing endonuclease sites, recombination sites or any combinations thereof. Any number of genes can be present. FIGS. 1 and 2 show mini-chromosome vector structures with 2 and 4 genes, respectively.

The mini-chromosome vector may also contain a bacterial plasmid backbone for propagation of the plasmid in bacteria such as E. coli, A. tumefaciens, or A. rhizogenes. The plasmid backbone may be that of a low-copy vector or in other embodiments it may be desirable to use a mid to high level copy backbone. In one embodiment of the invention, this backbone contains the replicon of the F′ plasmid of E. coli. However, other plasmid replicons, such as the bacteriophage P1 replicon, or other low-copy plasmid systems such as the RK2 replication origin, may also be used. The backbone may include one or several antibiotic-resistance genes conferring resistance to a specific antibiotic to the bacterial cell in which the plasmid is present. Bacterial antibiotic-resistance genes include but are not limited to kanamycin-, ampicillin-, chloramphenicol-, streptomycin-, spectinomycin-, tetracycline- and gentamycin-resistance genes.

The mini-chromosome vector may also contain plant telomeres. An exemplary telomere sequence is TTTAGGG or its complement. Telomeres are specialized DNA structures at the ends of linear chromosomes that function to stabilize the ends and facilitate the complete replication of the extreme termini of the DNA molecule (Richards et. al., Cell. 1988 Apr. 8; 53(1):127-36; Ausubel et al., Current Protocols in Molecular Biology, Wiley & Sons, 1997).

Additionally, the mini-chromosome vector may contain “stuffer DNA” sequences that serve to separate the various components on the mini-chromosome (centromere, genes, telomeres) from each other. The stuffer DNA may be of any origin, prokaryotic or eukaryotic, and from any genome or species, plant, animal, microbe or organelle, or may be of synthetic origin. The stuffer DNA can range from 100 bp to 10 Mb in length and can be repetitive in sequence, with unit repeats from 10 to 1,000,000 bp. Examples of repetitive sequences that can be used as stuffer DNAs include but are not limited to: rDNA, satellite repeats, retroelements, transposes, pseudogenes, transcribed genes, microsatellites, tDNA genes, short sequence repeats and combinations thereof. Alternatively, the stuffer DNA can consist of unique, non-repetitive DNA of any origin or sequence. The stuffer sequences may also include DNA with the ability to form boundary domains, such as but not limited to scaffold attachment regions (SARs) or matrix attachment regions (MARs). The stuffer DNA may be entirely synthetic, composed of random sequence. In this case, the stuffer DNA may have any base composition, or any A/T or G/C content. For example, the G/C content of the stuffer DNA could resemble that of the plant (˜30-40%), or could be much lower (0-30%) or much higher (40-100%). Alternatively, the stuffer sequences could be synthesized to contain an excess of any given nucleotide such as A, C, G or T. Different synthetic stuffers of different compositions may also be combined with each other. For example a fragment with low G/C content may be flanked or abutted by a fragment of medium or high G/C content, or vice versa.

In one embodiment of the invention, the mini-chromosome has a circular structure without telomeres, as shown in FIGS. 1 and 2 “circular”. In another embodiment, the mini-chromosome has a circular structure with telomeres, as shown in FIGS. 1 and 2 “linear”. In a third embodiment, the mini-chromosome has a linear structure with telomeres, as would result if the “linear” structure shown in FIGS. 1 and 2 were to be cut with a unique endonuclease, exposing the telomeres at the ends of a DNA molecule that contains all of the sequence contained in the original, closed construct with the exception of the antibiotic-resistance gene #1. In a fourth embodiment of the invention, the telomeres could be placed in such a manner that the bacterial replicon, backbone sequences, antibiotic-resistance genes and any other sequences of bacterial origin and present for the purposes of propagation of the mini-chromosome in bacteria, can be removed from the plant-expressed genes, the centromere, telomeres, and other sequences by cutting the structure with unique endonuclease #2 (FIG. 3). This results in a mini-chromosome from which much of, or preferably all, bacterial sequences have been removed. In this embodiment, bacterial sequence present between or among the plant-expressed genes or other mini-chromosome sequences would be excised prior to removal of the remaining bacterial sequences by cutting the mini-chromosome with homing endonuclease #1, and re-ligating the structure such that the antibiotic-resistance gene #1 has been lost (FIG. 3). In all of the structures shown in FIGS. 1, 2 and 3, the unique endonuclease site may be the recognition sequence of a homing endonuclease. Alternatively, the endonucleases and their sites can be replaced with any specific DNA cutting mechanism and its specific recognition site such as rare-cutting endonuclease or recombinase and its specific recognition site, as long as that site is present in the mini-chromosomes only at the indicated positions.

Various structural configurations are possible by which mini-chromosome elements can be oriented with respect to each other. A centromere can be placed on a mini-chromosome either between genes or outside a cluster of genes next to one telomere or next to the other telomere. Stuffer DNAs can be combined with these configurations to place the stuffer sequences inside the telomeres, around the centromere between genes or any combination thereof. Thus, a large number of alternative mini-chromosome structures are possible, depending on the relative placement of centromere DNA, genes, stuffer DNAs, bacterial sequences, telomeres, and other sequences. The sequence content of each of these variants is the same, but their structure may be different depending on how the sequences are placed. These variations in architecture are possible both for linear and for circular mini-chromosomes.

Exemplary Centromere Components

Centromere components may be isolated or derived from native plant genome, for example, modified through recombinant techniques or through the cell-based techniques described below. Alternatively, wholly artificial centromere components may be constructed using as a general guide the sequence of native centromeres. Combinations of centromere components derived from natural sources and/or combinations of naturally derived and artificial components are also contemplated As noted above, centromere sequence from one taxonomic plant species has been shown to be functional in another taxonomic plant species, genus and family.

In one embodiment, the centromere contains n copies of a repeated nucleotide sequence obtained by the methods disclosed herein, wherein n is at least 2. In another embodiment, the centromere contains n copies of interdigitated repeats. An interdigitated repeat is a DNA sequence that consists of two distinct repetitive elements that combine to create an unique permutation. Potentially any number of repeat copies capable of physically being placed on the recombinant construct could be included on the construct, including about 5, 10, 15, 20, 30, 50, 75, 100, 150, 200, 300, 400, 500, 750, 1,000, 1,500, 2,000, 3,000, 5,000, 7,500, 10,000, 20,000, 30,000, 40,000, 50,000, 60,000, 70,000, 80,000, 90,000 and about 100,000, including all ranges in-between such copy numbers. Moreover, the copies, while largely identical, can vary from each other. Such repeat variation is commonly observed in naturally occurring centromeres. The length of the repeat may vary, but will preferably range from about 20 bp to about 360 bp, from about 20 bp to about 250 bp, from about 50 bp to about 225 bp, from about 75 bp to about 210 bp, such as a 92 bp repeat and a 97 bp repeat, from about 100 bp to about 205 bp, from about 125 bp to about 200 bp, from about 150 bp to about 195 bp, from about 160 bp to about 190 and from about 170 bp to about 185 bp including about 180 bp.

Modification of Centromeres Isolated from Native Plant Genome

Modification and changes may be made in the centromeric DNA segments of the current invention and still obtain a functional molecule with desirable characteristics. The following is a discussion based upon changing the nucleic acids of a centromere to create an equivalent, or even an improved, second generation molecule.

In particular embodiments of the invention, mutated centromeric sequences are contemplated to be useful for increasing the utility of the centromere. It is specifically contemplated that the function of the centromeres of the current invention may be based in part of in whole upon the secondary structure of the DNA sequences of the centromere, modification of the DNA with methyl groups or other adducts, and/or the proteins which interact with the centromere. By changing the DNA sequence of the centromere, one may alter the affinity of one or more centromere-associated protein(s) for the centromere and/or the secondary structure or modification of the centromeric sequences, thereby changing the activity of the centromere. Alternatively, changes may be made in the centromeres of the invention which do not affect the activity of the centromere. Changes in the centromeric sequences which reduce the size of the DNA segment needed to confer centromere activity are contemplated to be particularly useful in the current invention, as would changes which increased the fidelity with which the centromere was transmitted during mitosis and meiosis.

Modification of Centromeres by Passage Through Bacteria, Plant or Other Hosts or Processes

In the methods of the present invention, the resulting mini-chromosome DNA sequence may also be a derivative of the parental clone or centromere clone having substitutions, deletions, insertions, duplications and/or rearrangements of one or more nucleotides in the nucleic acid sequence. Such nucleotide mutations may occur individually or consecutively in stretches of 1, 2, 3, 4, 5, 10, 20, 40, 80, 100, 200, 400, 800, 1000, 2000, 4000, 8000, 10000, 50000, 100000, and about 200000, including all ranges in-between.

Variations of mini-chromosomes may arise through passage of mini-chromosomes through various hosts including virus, bacteria, yeast, plant or other prokaryotic or eukaryotic organism and may occur through passage of multiple hosts or individual host. Variations may also occur by replicating the mini-chromosome in vitro.

Derivatives may be identified through sequence analysis, or variations in mini-chromosome molecular weight through electrophoresis such as, but not limited to, CHEF gel analysis, column or gradient separation, or any other methods used in the field to determine and/or analyze DNA molecular weight or sequence content. Alternately, derivatives may be identified by the altered activity of a derivative in conferring centromere function to a mini-chromosome.

Exemplary Exogenous Nucleic Acids Including Plant-Expressed Genes

Of particular interest in the present invention are exogenous nucleic acids which when introduced into plants alter the phenotype of the plant, a plant organ, plant tissue, or portion of the plant. Exemplary exogenous nucleic acids encode polypeptides involved in one or more important biological properties in plants. Other exemplary exogenous nucleic acids alter expression of exogenous or endogenous genes, either increasing or decreasing expression, optionally in response to a specific signal or stimulus.

As used herein, the term “trait” can refer either to the altered phenotype of interest or the nucleic acid which causes the altered phenotype of interest.

One of the major purposes of transformation of crop plants is to add some commercially desirable, agronomically important traits to the plant. Such traits include, but are not limited to, herbicide resistance or tolerance; insect (pest) resistance or tolerance; disease resistance or tolerance (viral, bacterial, fungal, nematode or other pathogens); stress tolerance and/or resistance, as exemplified by resistance or tolerance to drought, heat, chilling, freezing, excessive moisture, salt stress, mechanical stress, extreme acidity, alkalinity, toxins, UV light, ionizing radiation or oxidative stress; increased yields, whether in quantity or quality; enhanced or altered nutrient acquisition and enhanced or altered metabolic efficiency; enhanced or altered nutritional content and makeup of plant tissues used for food, feed, fiber or processing; physical appearance; male sterility; drydown; standability; prolificacy; starch quantity and quality; oil quantity and quality; protein quality and quantity; amino acid composition; modified chemical production; altered pharmaceutical or nutraceutical properties; altered bioremediation properties; increased biomass; altered growth rate; altered fitness; altered biodegradability; altered CO₂ fixation; presence of bioindicator activity; altered digestibility by humans or animals; altered allergenicity; altered mating characteristics; altered pollen dispersal; improved environmental impact; altered nitrogen fixation capability; the production of a pharmaceutically active protein; the production of a small molecule with medicinal properties; the production of a chemical including those with industrial utility; the production of nutraceuticals, food additives, carbohydrates, RNAs, lipids, fuels, dyes, pigments, vitamins, scents, flavors, vaccines, antibodies, hormones, and the like; and alterations in plant architecture or development, including changes in developmental timing, photosynthesis, signal transduction, cell growth, reproduction, or differentiation. Additionally one could create a library of an entire genome from any organism or organelle including mammals, plants, microbes, fungi, or bacteria, represented on mini-chromosomes.

In one embodiment, the modified plant may exhibit increased or decreased expression or accumulation of a product of the plant, which may be a natural product of the plant or a new or altered product of the plant. Exemplary products include an enzyme, an RNA molecule, a nutritional protein, a structural protein, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a phenylpropanoid, or terpenoid, a steroid, a flavonoid, a phenolic compound, an anthocyanin, a pigment, a vitamin or a plant hormone. In another embodiment, the modified plant has enhanced or diminished requirement for light, water, nitrogen, or trace elements. In another embodiment the modified plant has an enhance ability to capture or fix nitrogen from its environment. In yet another embodiment, the modified plant is enriched for an essential amino acid as a proportion of a protein fraction of the plant. The protein fraction may be, for example, total seed protein, soluble protein, insoluble protein, water-extractable protein, and lipid-associated protein. The modification may include overexpression, underexpression, antisense modulation, sense suppression, inducible expression, inducible repression, or inducible modulation of a gene.

A brief summary of exemplary improved properties and polypeptides of interest for either increased or decreased expression is provided below.

(i) Herbicide Resistance

A herbicide resistance (or tolerance) trait is a characteristic of a modified plant that is resistant to dosages of an herbicide that is typically lethal to a non-modified plant. Exemplary herbicides for which resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and glufosinate herbicides. Other herbicides would be useful as would combinations of herbicide genes on the same mini-chromosome.

The genes encoding phosphinothricin acetyltransferase (bar), glyphosate tolerant EPSP synthase genes, glyphosate acetyltransferase, the glyphosate degradative enzyme gene gox encoding glyphosate oxidoreductase, deh (encoding a dehalogenase enzyme that inactivates dalapon), herbicide resistant (e.g., sulfonylurea and imidazolinone) acetolactate synthase, and bxn genes (encoding a nitrilase enzyme that degrades bromoxynil) are good examples of herbicide resistant genes for use in transformation. The bar gene codes for an enzyme, phosphinothricin acetyltransferase (PAT), which inactivates the herbicide phosphinothricin and prevents this compound from inhibiting glutamine synthetase enzymes. The enzyme 5 enolpyruvylshikimate 3 phosphate synthase (EPSP Synthase), is normally inhibited by the herbicide N (phosphonomethyl)glycine (glyphosate). However, genes are known that encode glyphosate resistant EPSP synthase enzymes. These genes are particularly contemplated for use in plant transformation. The deh gene encodes the enzyme dalapon dehalogenase and confers resistance to the herbicide dalapon. The bxn gene codes for a specific nitrilase enzyme that converts bromoxynil to a non herbicidal degradation product. The glyphosate acetyl transferase gene inactivates the herbicide glyphosate and prevents this compound from inhibiting EPSP synthase.

Polypeptides that may produce plants having tolerance to plant herbicides include polypeptides involved in the shikimate pathway, which are of interest for providing glyphosate tolerant plants. Such polypeptides include polypeptides involved in biosynthesis of chorismate, phenylalanine, tyrosine and tryptophan.

(ii) Insect Resistance

Potential insect resistance (or tolerance) genes that can be introduced include Bacillus thuringiensis crystal toxin genes or Bt genes (Watrud et al., In: Engineered Organisms and the Environment, 1985). Bt genes may provide resistance to lepidopteran or coleopteran pests such as European Corn Borer (ECB). Preferred Bt toxin genes for use in such embodiments include the CryIA(b) and CryIA(c) genes. Endotoxin genes from other species of B. thuringiensis which affect insect growth or development also may be employed in this regard.

It is contemplated that preferred Bt genes for use in the mini-chromosomes disclosed herein will be those in which the coding sequence has been modified to effect increased expression in plants, and for example, in monocot plants. Means for preparing synthetic genes are well known in the art and are disclosed in, for example, U.S. Pat. No. 5,500,365 and U.S. Pat. No. 5,689,052, each of the disclosures of which are specifically incorporated herein by reference in their entirety. Examples of such modified Bt toxin genes include a synthetic Bt CryIA(b) gene (Perlak et al., Proc. Natl. Acad. Sci. USA, 88:3324-3328, 1991), and the synthetic CryIA(c) gene termed 1800b (PCT Application WO 95/06128). Some examples of other Bt toxin genes known to those of skill in the art are given in Table 1 below.

TABLE 1 Bacillus thuringiensis Endotoxin Genes^(a) New Nomenclature Old Nomenclature GenBank Accession Cry1Aa Cry1A(a) M11250 Cry1Ab Cry1A(b) M13898 Cry1Ac Cry1A(c) M11068 Cry1Ad Cry1A(d) M73250 Cry1Ae Cry1A(e) M65252 Cry1Ba Cry1B X06711 Cry1Bb ET5 L32020 Cry1Bc PEG5 Z46442 Cry1Bd CryEI U70726 Cry1Ca Cry1C X07518 Cry1Cb Cry1C(b) M97880 Cry1Da Cry1D X54160 Cry1Db PrtB Z22511 Cry1Ea Cry1E X53985 Cry1Eb Cry1E(b) M73253 Cry1Fa Cry1F M63897 Cry1Fb PrtD Z22512 Cry1Ga PrtA Z22510 Cry1Gb CryH2 U70725 Cry1Ha PrtC Z22513 Cry1Hb U35780 Cry1Ia CryV X62821 CryIib CryV U07642 Cry1Ja ET4 L32019 Cry1Jb ET1 U31527 Cry1K U28801 Cry2Aa Cry1IA M31738 Cry2Ab Cry1IB M23724 Cry2Ac Cry1IC X57252 Cry3A Cry1IIA M22472 Cry3Ba Cry1IIB X17123 Cry3Bb CryIIIB2 M89794 Cry3C Cry1IID X59797 Cry4A Cry1VA Y00423 Cry4B Cry1VB X07423 Cry5Aa CryVA(a) L07025 Cry5Ab CryVA(b) L07026 Cry6A CryVIA L07022 Cry6B CryVIB L07024 Cry7Aa Cry1IIC M64478 Cry7Ab Cry1IICb U04367 Cry8A Cry1IIE U04364 Cry8B Cry1IIG U04365 Cry8C Cry1IIF U04366 Cry9A Cry1G X58120 Cry9B CryIX X75019 Cry9C Cry1H Z37527 Cry1OA Cry1VC M12662 Cry1IA Cry1VD M31737 Cry1IB Jeg80 X86902 Cry12A CryVB L07027 Cry13A CryVC L07023 Cry14A CryVD U13955 Cry15A 34 kDa M76442 Cry16A cbm71 X94146 Cry17A cbm71 X99478 Cry18A CryBPI X99049 Cry19A Jeg65 Y08920 CytIAa CytA X03182 CytIAb CytM X98793 Cyt2A CytB Z14147 Cyt2B CytB U52043 ^(a)Adapted from: Crickmore, N, Zeigler, D R, Feitelson, J. et al. 1998. Revision of the Nomenclature for the Bacillus thuringiensis Pesticidal Crystal Proteins. Microbiol. Molec. Biol. Rev. 62: 807-813.

Protease inhibitors also may provide insect resistance (Johnson et al., Proc Natl Acad Sci USA. 1989 December; 86(24): 9871-9875.), and will thus have utility in plant transformation. The use of a protease inhibitor II gene, pinII, from tomato or potato is envisioned to be particularly useful. Even more advantageous is the use of a pinII gene in combination with a Bt toxin gene, the combined effect of which has been discovered to produce synergistic insecticidal activity. Other genes which encode inhibitors of the insect's digestive system, or those that encode enzymes or co factors that facilitate the production of inhibitors, also may be useful. This group may be exemplified by oryzacystatin and amylase inhibitors such as those from wheat and barley.

Amylase inhibitors are found in various plant species and are used to ward off insect predation via inhibition of the digestive amylases of attacking insects. Several amylase inhibitor genes have been isolated from plants and some have been introduced as exogenous nucleic acids, conferring an insect resistant phenotype that is potentially useful (“Plants, Genes, and Crop Biotechnology” by Maarten J. Chrispeels and David E. Sadava (2003) Jones and Bartlett Press).

Genes encoding lectins may confer additional or alternative insecticide properties. Lectins are multivalent carbohydrate binding proteins which have the ability to agglutinate red blood cells from a range of species. Lectins have been identified recently as insecticidal agents with activity against weevils, ECB and rootworm (Murdock et al., Phytochemistry, 29:85-89, 1990, Czapla & Lang, J. Econ. Entomol., 83:2480-2485, 1990). Lectin genes contemplated to be useful include, for example, barley and wheat germ agglutinin (WGA) and rice lectins (Gatehouse et al., J. Sci. Food. Agric., 35:373-380, 1984), with WGA being preferred.

Genes controlling the production of large or small polypeptides active against insects when introduced into the insect pests, such as, e.g., lytic peptides, peptide hormones and toxins and venoms, form another aspect of the invention. For example, it is contemplated that the expression of juvenile hormone esterase, directed towards specific insect pests, also may result in insecticidal activity, or perhaps cause cessation of metamorphosis (Hammock et al., Nature, 344:458-461, 1990).

Genes which encode enzymes that affect the integrity of the insect cuticle form yet another aspect of the invention. Such genes include those encoding, e.g., chitinase, proteases, lipases and also genes for the production of nikkomycin, a compound that inhibits chitin synthesis, the introduction of any of which is contemplated to produce insect resistant plants. Genes that code for activities that affect insect molting, such as those affecting the production of ecdysteroid UDP glucosyl transferase, also fall within the scope of the useful exogenous nucleic acids of the present invention.

Genes that code for enzymes that facilitate the production of compounds that reduce the nutritional quality of the host plant to insect pests also are encompassed by the present invention. It may be possible, for instance, to confer insecticidal activity on a plant by altering its sterol composition. Sterols are obtained by insects from their diet and are used for hormone synthesis and membrane stability. Therefore alterations in plant sterol composition by expression of novel genes, e.g., those that directly promote the production of undesirable sterols or those that convert desirable sterols into undesirable forms, could have a negative effect on insect growth and/or development and hence endow the plant with insecticidal activity. Lipoxygenases are naturally occurring plant enzymes that have been shown to exhibit anti nutritional effects on insects and to reduce the nutritional quality of their diet. Therefore, further embodiments of the invention concern modified plants with enhanced lipoxygenase activity which may be resistant to insect feeding.

Tripsacum dactyloides is a species of grass that is resistant to certain insects, including corn root-worm. It is anticipated that genes encoding proteins that are toxic to insects or are involved in the biosynthesis of compounds toxic to insects will be isolated from Tripsacum and that these novel genes will be useful in conferring resistance to insects. It is known that the basis of insect resistance in Tripsacum is genetic, because said resistance has been transferred to Zea mays via sexual crosses (Branson and Guss, Proceedings North Central Branch Entomological Society of America, 27:91-95, 1972). It is further anticipated that other cereal, monocot or dicot plant species may have genes encoding proteins that are toxic to insects which would be useful for producing insect resistant plants.

Further genes encoding proteins characterized as having potential insecticidal activity also may be used as exogenous nucleic acids in accordance herewith. Such genes include, for example, the cowpea trypsin inhibitor (CpTI; Hilder et al., Nature, 330:160-163, 1987) which may be used as a rootworm deterrent; genes encoding avermectin (Avermectin and Abamectin., Campbell, W. C., Ed., 1989; Ikeda et al., J. Bacteriol., 169:5615-5621, 1987) which may prove particularly useful as a corn rootworm deterrent; ribosome inactivating protein genes; and even genes that regulate plant structures. Modified plants including anti insect antibody genes and genes that code for enzymes that can convert a non toxic insecticide (pro insecticide) applied to the outside of the plant into an insecticide inside the plant also are contemplated.

Polypeptides that may improve plant tolerance to effects of plant pests or pathogens include proteases, polypeptides involved in anthocyanin biosynthesis, polypeptides involved in cell wall metabolism, including cellulases, glucosidases, pectin methylesterase, pectinase, polygalacturonase, chitinase, chitosanase, and cellulose synthase, and polypeptides involved in biosynthesis of terpenoids or indole for production of bioactive metabolites to provide defense against herbivorous insects. It is also anticipated that combinations of different insect resistance genes on the same mini-chromosome will be particularly useful.

Vegetative Insecticidal Proteins (VIP) are a relatively new class of proteins originally found to be produced in the vegetative growth phase of the bacterium, Bacillus cereus, but do have a spectrum of insect lethality similar to the insecticidal genes found in strains of Bacillus thuriengensis. Both the vip1a and vip3A genes have been isolated and have demonstrated insect toxicity. It is anticipated that such genes may be used in modified plants to confer insect resistance (“Plants, Genes, and Crop Biotechnology” by Maarten J. Chrispeels and David E. Sadava (2003) Jones and Bartlett Press).

(iii) Environment or Stress Resistance

Improvement of a plant's ability to tolerate various environmental stresses such as, but not limited to, drought, excess moisture, chilling, freezing, high temperature, salt, and oxidative stress, also can be effected through expression of novel genes. It is proposed that benefits may be realized in terms of increased resistance to freezing temperatures through the introduction of an “antifreeze” protein such as that of the Winter Flounder (Cutler et al., J. Plant Physiol., 135:351-354, 1989) or synthetic gene derivatives thereof. Improved chilling tolerance also may be conferred through increased expression of glycerol 3 phosphate acetyltransferase in chloroplasts (Wolter et al., The EMBO J., 4685-4692, 1992). Resistance to oxidative stress (often exacerbated by conditions such as chilling temperatures in combination with high light intensities) can be conferred by expression of superoxide dismutase (Gupta et al., 1993), and may be improved by glutathione reductase (Bowler et al., Ann Rev. Plant Physiol., 43:83-116, 1992). Such strategies may allow for tolerance to freezing in newly emerged fields as well as extending later maturity higher yielding varieties to earlier relative maturity zones.

It is contemplated that the expression of novel genes that favorably affect plant water content, total water potential, osmotic potential, or turgor will enhance the ability of the plant to tolerate drought. As used herein, the terms “drought resistance” and “drought tolerance” are used to refer to a plant's increased resistance or tolerance to stress induced by a reduction in water availability, as compared to normal circumstances, and the ability of the plant to function and survive in lower water environments. In this aspect of the invention it is proposed, for example, that the expression of genes encoding for the biosynthesis of osmotically active solutes, such as polyol compounds, may impart protection against drought. Within this class are genes encoding for mannitol L phosphate dehydrogenase (Lee and Saier, 1982) and trehalose 6 phosphate synthase (Kaasen et al., J. Bacteriology, 174:889-898, 1992). Through the subsequent action of native phosphatases in the cell or by the introduction and coexpression of a specific phosphatase, these introduced genes will result in the accumulation of either mannitol or trehalose, respectively, both of which have been well documented as protective compounds able to mitigate the effects of stress. Mannitol accumulation in transgenic tobacco has been verified and preliminary results indicate that plants expressing high levels of this metabolite are able to tolerate an applied osmotic stress (Tarczynski et al., Science, 259:508-510, 1993, Tarczynski et al Proc. Natl. Acad. Sci. USA, 89:1-5, 1993).

Similarly, the efficacy of other metabolites in protecting either enzyme function (e.g., alanopine or propionic acid) or membrane integrity (e.g., alanopine) has been documented (Loomis et al., J. Expt. Zoology, 252:9-15, 1989), and therefore expression of genes encoding for the biosynthesis of these compounds might confer drought resistance in a manner similar to or complimentary to mannitol. Other examples of naturally occurring metabolites that are osmotically active and/or provide some direct protective effect during drought and/or desiccation include fructose, erythritol (Coxson et al., Biotropica, 24:121-133, 1992), sorbitol, dulcitol (Karsten et al., Botanica Marina, 35:11-19, 1992), glucosyiglycerol (Reed et al., J. Gen. Microbiology, 130:1-4, 1984; Erdmann et al., J. Gen. Microbiology, 138:363-368, 1992), sucrose, stachyose (Koster and Leopold, Plant Physiol., 88:829-832, 1988; Blackman et al., Plant Physiol., 100:225-230, 1992), raffinose (Bernal Lugo and Leopold, Plant Physiol., 98:1207-1210, 1992), proline (Rensburg et al., J. Plant Physiol., 141:188-194, 1993), glycine betaine, ononitol and pinitol (Vernon and Bohnert, The EMBO J., 11:2077-2085, 1992). Continued canopy growth and increased reproductive fitness during times of stress will be augmented by introduction and expression of genes such as those controlling the osmotically active compounds discussed above and other such compounds. Currently preferred genes which promote the synthesis of an osmotically active polyol compound are genes which encode the enzymes mannitol 1 phosphate dehydrogenase, trehalose 6 phosphate synthase and myoinositol 0 methyltransferase.

It is contemplated that the expression of specific proteins also may increase drought tolerance. Three classes of Late Embryogenic Proteins have been assigned based on structural similarities (see Dure et al., Plant Molecular Biology, 12:475-486, 1989). All three classes of LEAs have been demonstrated in maturing (e.g. desiccating) seeds. Within these 3 types of LEA proteins, the Type II (dehydrin type) have generally been implicated in drought and/or desiccation tolerance in vegetative plant parts (e.g. Mundy and Chua, The EMBO J., 7:2279-2286, 1988; Piatkowski et al., Plant Physiol., 94:1682-1688, 1990; Yamaguchi Shinozaki et al., Plant Cell Physiol., 33:217-224, 1992). Expression of a Type III LEA (HVA 1) in tobacco was found to influence plant height, maturity and drought tolerance (Fitzpatrick, Gen. Engineering News, 22:7, 1993). In rice, expression of the HVA 1 gene influenced tolerance to water deficit and salinity (Xu et al., Plant Physiol., 110:249-257, 1996). Expression of structural genes from any of the three LEA groups may therefore confer drought tolerance. Other types of proteins induced during water stress include thiol proteases, aldolases or transmembrane transporters (Guerrero et al., Plant Molecular Biology, 15:11-26, 1990), which may confer various protective and/or repair type functions during drought stress. It also is contemplated that genes that effect lipid biosynthesis and hence membrane composition might also be useful in conferring drought resistance on the plant.

Many of these genes for improving drought resistance have complementary modes of action. Thus, it is envisaged that combinations of these genes might have additive and/or synergistic effects in improving drought resistance in plants. Many of these genes also improve freezing tolerance (or resistance); the physical stresses incurred during freezing and drought are similar in nature and may be mitigated in similar fashion. Benefit may be conferred via constitutive expression of these genes, but the preferred means of expressing these novel genes may be through the use of a turgor induced promoter (such as the promoters for the turgor induced genes described in Guerrero et al., Plant Molecular Biology, 15:11-26, 1990 and Shagan et al., Plant Physiol., 101:1397-1398, 1993 which are incorporated herein by reference). Spatial and temporal expression patterns of these genes may enable plants to better withstand stress.

It is proposed that expression of genes that are involved with specific morphological traits that allow for increased water extractions from drying soil would be of benefit. For example, introduction and expression of genes that alter root characteristics may enhance water uptake. It also is contemplated that expression of genes that enhance reproductive fitness during times of stress would be of significant value. For example, expression of genes that improve the synchrony of pollen shed and receptiveness of the female flower parts, e.g., silks, would be of benefit. In addition it is proposed that expression of genes that minimize kernel abortion during times of stress would increase the amount of grain to be harvested and hence be of value.

Given the overall role of water in determining yield, it is contemplated that enabling plants to utilize water more efficiently, through the introduction and expression of novel genes, will improve overall performance even when soil water availability is not limiting. By introducing genes that improve the ability of plants to maximize water usage across a full range of stresses relating to water availability, yield stability or consistency of yield performance may be realized.

Polypeptides that may improve stress tolerance under a variety of stress conditions include polypeptides involved in gene regulation, such as serine/threonine-protein kinases, MAP kinases, MAP kinase kinases, and MAP kinase kinase kinases; polypeptides that act as receptors for signal transduction and regulation, such as receptor protein kinases; intracellular signaling proteins, such as protein phosphatases, GTP binding proteins, and phospholipid signaling proteins; polypeptides involved in arginine biosynthesis; polypeptides involved in ATP metabolism, including for example ATPase, adenylate transporters, and polypeptides involved in ATP synthesis and transport; polypeptides involved in glycine betaine, jasmonic acid, flavonoid or steroid biosynthesis; and hemoglobin. Enhanced or reduced activity of such polypeptides in modified plants will provide changes in the ability of a plant to respond to a variety of environmental stresses, such as chemical stress, drought stress and pest stress.

Other polypeptides that may improve plant tolerance to cold or freezing temperatures include polypeptides involved in biosynthesis of trehalose or raffinose, polypeptides encoded by cold induced genes, fatty acyl desaturases and other polypeptides involved in glycerolipid or membrane lipid biosynthesis, which find use in modification of membrane fatty acid composition, alternative oxidase, calcium-dependent protein kinases, LEA proteins or uncoupling protein.

Other polypeptides that may improve plant tolerance to heat include polypeptides involved in biosynthesis of trehalose, polypeptides involved in glycerolipid biosynthesis or membrane lipid metabolism (for altering membrane fatty acid composition), heat shock proteins or mitochondrial NDK.

Other polypeptides that may improve tolerance to extreme osmotic conditions include polypeptides involved in proline biosynthesis.

Other polypeptides that may improve plant tolerance to drought conditions include aquaporins, polypeptides involved in biosynthesis of trehalose or wax, LEA proteins or invertase.

(iv) Disease Resistance

It is proposed that increased resistance (or tolerance) to diseases may be realized through introduction of genes into plants, for example, into monocotyledonous plants such as maize. It is possible to produce resistance to diseases caused by viruses, viroids, bacteria, fungi and nematodes. It also is contemplated that control of mycotoxin producing organisms may be realized through expression of introduced genes. Resistance can be effected through suppression of endogenous factors that encourage disease-causing interactions, expression of exogenous factors that are toxic to or otherwise provide protection from pathogens, or expression of factors that enhance the plant's own defense responses.

Resistance to viruses may be produced through expression of novel genes. For example, it has been demonstrated that expression of a viral coat protein in a modified plant can impart resistance to infection of the plant by that virus and perhaps other closely related viruses (Cuozzo et al., Bio/Technology, 6:549-553, 1988, Hemenway et al., The EMBO J., 7:1273-1280, 1988, Abel et al., Science, 232:738-743, 1986). It is contemplated that expression of antisense genes targeted at essential viral functions may also impart resistance to viruses. For example, an antisense gene targeted at the gene responsible for replication of viral nucleic acid may inhibit replication and lead to resistance to the virus. It is believed that interference with other viral functions through the use of antisense genes also may increase resistance to viruses. Further, it is proposed that it may be possible to achieve resistance to viruses through other approaches, including, but not limited to the use of satellite viruses.

It is proposed that increased resistance to diseases caused by bacteria and fungi may be realized through introduction of novel genes. It is contemplated that genes encoding so called “peptide antibiotics,” pathogenesis related (PR) proteins, toxin resistance, or proteins affecting host pathogen interactions such as morphological characteristics will be useful. Peptide antibiotics are polypeptide sequences which are inhibitory to growth of bacteria and other microorganisms. For example, the classes of peptides referred to as cecropins and magainins inhibit growth of many species of bacteria and fungi. It is proposed that expression of PR proteins in plants, for example, monocots such as maize, may be useful in conferring resistance to bacterial disease. These genes are induced following pathogen attack on a host plant and have been divided into at least five classes of proteins (Bol, Linthorst, and Cornelissen, 1990). Included amongst the PR proteins are beta 1, 3 glucanases, chitinases, and osmotin and other proteins that are believed to function in plant resistance to disease organisms. Other genes have been identified that have antifungal properties, e.g., UDA (stinging nettle lectin), or hevein (Broakaert et al., 1989; Barkai Golan et al., 1978). It is known that certain plant diseases are caused by the production of phytotoxins. It is proposed that resistance to these diseases would be achieved through expression of a novel gene that encodes an enzyme capable of degrading or otherwise inactivating the phytotoxin. It also is contemplated that expression of novel genes that alter the interactions between the host plant and pathogen may be useful in reducing the ability of the disease organism to invade the tissues of the host plant, e.g., an increase in the waxiness of the leaf cuticle or other morphological characteristics.

Polypeptides useful for imparting improved disease responses to plants include polypeptides encoded by cercosporin induced genes, antifungal proteins and proteins encoded by R-genes or SAR genes.

Agronomically important diseases caused by fungal phytopathogens include: glume or leaf blotch, late blight, stalk/head rot, rice blast, leaf blight and spot, corn smut, wilt, sheath blight, stem canker, root rot, blackleg or kernel rot.

Exemplary plant viruses include tobacco or cucumber mosaic virus, ringspot virus, necrosis virus, maize dwarf mosaic virus, etc. Specific fungal, bacterial and viral pathogens of major crops include, but are not limited to:

RICE: rice brown spot fungus (Cochliobolus miyabeanus), rice blast fungus—Magnaporthe grisea (Pyricularia grisea), Magnaporthe salvinii (Sclerotium oryzae), Xanthomomas oryzae pv. oryzae, Xanthomomas oryzae pv. oryzicola, Rhizoctonia spp. (including but not limited to Rhizoctonia solani, Rhizoctonia oryzae and Rhizoctonia oryzae-sativae), Pseudomonas spp. (including but not limited to Pseudomonas plantarii, Pseudomonas avenae, Pseudomonas glumae, Pseudomonas fuscovaginae, Pseudomonas alboprecipitans, Pseudomonas syringae pv. panici, Pseudomonas syringae pv. syringae, Pseudomonas syringae pv. oryzae and Pseudomonas syringae pv. aptata), Erwinia spp. (including but not limited to Erwinia herbicola, Erwinia amylovaora, Erwinia chrysanthemi and Erwinia carotovora), Achyla spp. (including but not limited to Achyla conspicua and Achyia klebsiana), Pythium spp. (including but not limited to Pythium dissotocum, Pythium irregulare, Pythium arrhenomanes, Pythium myriotylum, Pythium catenulatum, Pythium graminicola and Pythium spinosum), Saprolegnia spp., Dictyuchus spp., Pythiogeton spp., Phytophthora spp., Alternaria padwickii, Cochliobolus miyabeanus, Curvularia spp. (including but not limited to Curvularia lunata, Curvularia affinis, Curvularia clavata, Curvularia eragrostidis, Curvularia fallax, Curvularia geniculata, Curvularia inaequalis, Curvularia intermedia, Curvularia oryzae, Curvularia oryzae-sativae, Curvularia pallescens, Curvularia senegalensis, Curvularia tuberculata, Curvularia uncinata and Curvularia verruculosa), Sarocladium oryzae, Gerlachia oryzae, Fusarium spp. (including but not limited Fusarium graminearum, Fusarium nivale and to different pathovars of Fusarium monoliforme, including pvs. fujikuroi and zeae), Sclerotium rolfsii, Phoma exigua, Mucor fragilis, Trichoderma viride, Rhizopus spp., Cercospora oryzae, Entyloma oryzae, Dreschlera gigantean, Scierophthora macrospora, Mycovellosiella oryzae, Phomopsis oryzae-sativae, Puccinia graminis, Uromyces coronatus, Cylindrocladium scopariurn, Sarocladium oryzae, Gaeumannomyces graminis pv. graminis, Myrothecium verrucaria, Pyrenochaeta oryzae, Ustilaginoidea virens, Neovossia spp. (including but not limited to Neovossia horrida), Tilletia spp., Balansia oryzae-sativae, Phoma spp. (including but not limited to Phoma sorghina, Phoma insidiosa, Phoma glumarum, Phoma glumicola and Phoma oryzina), Nigrospora spp. (including but not limited to Nigrospora oryzae, Nigrospora sphaerica, Nigrospora panici and Nigrospora padwickii), Epiococcum nigrum, Phyllostica spp., Wolkia decolorans, Monascus purpureus, Aspergillus spp., Penicillium spp., Absidia spp., Mucor spp., Chaetomium spp., Dematium spp., Monilia spp., Streptomyces spp., Syncephalastrum spp., Verticillium spp., Nematospora coryli, Nakataea sigmoidea, Cladosporium spp., Bipolaris spp., Coniothyrium spp., Diplodia oryzae, Exserophilum rostratum, Helococera oryzae, Melanomma glumarum, Metashaeria spp., Mycosphaerella spp., Oidium spp., Pestalotia spp., Phaeoseptoria spp., Sphaeropsis spp., Trematosphaerelia spp., rice black-streaked dwarf virus, rice dwarf virus, rice gall dwarf virus, barley yellow dwarf virus, rice grassy stunt virus, rice hoja blanca virus, rice necrosis mosaic virus, rice ragged stunt virus, rice stripe virus, rice stripe necrosis virus, rice transitory yellowing virus, rice tungro bacilliform virus, rice tungro spherical virus, rice yellow mottle virus, rice tarsonemid mite virus, Echinochloa hoja blanca virus, Echinochloa ragged stunt virus, orange leaf mycoplasma-like organism, yellow dwarf mycoplasma-like organism, Aphelenchoides besseyi, Ditylenchus angustus, Hirschmanniella spp., Criconemella spp., Meloidogyne spp., Heterodera spp., Pratylenchus spp., Hoplolaimus indicus.

SOYBEANS: Phytophthora sojae, Fusarium solani f. sp. Glycines, Macrophomina phaseolina, Fusarium, Pythium, Rhizoctonia, Phialophora gregata, Sclerotinia sclerotiorum, Diaporthe phaseolorum var. sojae, Colletotrichum truncatum, Phomopsis longicolla, Cercospora kikuchii, Diaporthe phaseolonum var. meridionalis (and var. caulivora), Phakopsora pachyrhyzi, Fusarium solani, Microsphaera diffusa, Septoria glycines, Cercospora kikuchii, Macrophomina phaseolina, Sclerotinia scierotiorum, Corynespora cassiicola, Rhizoctonia solani, Cercospora sojina, Phytophthora megasperma fsp. glycinea, Macrophomina phaseolina, Fusarium oxysporum, Diapothe phaseolorum var. sojae (Phomopsis sojae), Diaporthe phaseolorum var. caulivora, Sclerotium rolfsii, Cercospora kikuchii, Cercospora sojina, Peronospora manshurica, Colletotrichum dematium (Colletotichum truncatum), Corynespora cassiicola, Phyllosticta sojicola, Alternaria alternata, Pseudomonas syringae p.v. glycinea, Xanthomonas campestris p.v. phaseoli, Microspaera diffusa, Fusarium semitectum, Phialophora gregata, Soybean mosaic virus, Glomerella glycines, Tobacco Ring spot virus, Tobacco Streak virus, Phakopsora pachyrhizi, Pythium aphanidermatum, Pythium ultimum, Pythium dearyanum, Tomato spotted wilted virus, Heterodera glycines, Fusarium solani, Soybean cyst and root knot nematodes.

CORN: Fusarium moniliforme var. subglutinans, Erwinia stewartii, Fusarium moniliforme, Gibberella zeae (Fusarium Graminearum), Stenocarpella maydi (Diplodia maydis), Pythium irregulare, Pythium debaryanum, Pythium graminicola, Pythium splendens, Pythium ultimum, Pythium aphanidermatum, Aspergillus flavus, Bipolaris maydis O, T (cochliobolus heterostrophus), Helminthosporium carbonum I, II, and III (Cochliobolus carbonum), Exserohilum turcicum I, II and III, Helminthosporium pedicellatum, Physoderma maydis, Phyllosticta maydis, Kabatie-maydis, Cercospora sorghi, Ustilago maydis, Puccinia sorghi, Puccinia polysora, Macrophomina phaseolina, Penicillium oxalicum, Nigrospora oryzae, Cladosporium herbarum, Curvularia lunata, Curvularia inaequalis, Curvularia pallescens, Clavibacter michiganese subsp. Nebraskense, Trichoderma viride, Maize dwarf Mosaic Virus A and B, Wheat Streak Mosaic Virus, Maize Chlorotic Dwarf Virus, Claviceps sorghi, Pseudonomas avenae, Erwinia chrysantemi p.v. Zea, Erwinia corotovora, Cornstun spiroplasma, Diplodia macrospora, Sclerophthora macrospora, Peronosclerospora sorghi, Peronoscherospora philippinesis, Peronosclerospora maydis, Peronosclerospora sacchari, Spacelotheca reiliana, Physopella zea, Cephalosporium maydis, Cephalosporium acremonium, Maize Chlorotic Mottle Virus, High Plains Virus, Maize Mosaic Virus, Maize Rayado Fino Virus, Maize Streak Virus, Maize Stripe Virus, Maize Rought Dwarf Virus:

WHEAT: Pseudomonas syringae p.v. atrofaciens, Urocystis agropyri, Xanthomonas campestris p.v. translucens, Pseudomonas syringae p.v. syringae, Alternaria alternata, Cladosporium herbarum, Fusarium graminearum, Fusarium avenaceum, Fusarium culmorum, Ustilago tritici, Ascochyta tritici, Cephalosporium gramineum, Collotetrichum graminicola, Erysiphe graminis f. sp. Tritici, Puccinia graminis f. sp. Tritici, Puccinia recondite f. sp. tritici, puccinia striiformis, Pyrenophora triticirepentis, Septoria nodorum, Septoria tritici, Spetoria avenae, Pseudocercosporella herpotrichoides, Rhizoctonia solani, Rhizoctonia cerealis, Gaeumannomyces graminis var. tritici, Pythium aphanidermatum, Pythium arrhenomanes, Pythium ultimum, Bipolaris sorokiniana, Barley Yellow Dwarf Virus, Brome Mosaic Virus, Soil Borne Wheat Mosaic Virus, Wheat Streak Virus, Wheat Spindle Streak Virus, American Wheat Striate Virus, Claviceps purpurea, Tilletia tritici, Tilletia laevis, Pstilago tritici, Tilletia indica, Rhizoctonia solani, Pythium arrhenomannes, Pythium gramicola, Pythium aphanidermatum, High Plains Virus, European Wheat Striate Virus:

CANOLA: Albugo candida, Alternaria brassicae, Leptosharia maculans, Rhizoctonia solani, Sclerotinia sclerotiorum, Mycospaerella brassiccola, Pythium ultimum, Peronospora parasitica, Fusarium roseum, Fusarium oxysporum, Tilletia foetida, Tilletia caries, Alternaria alternata:

SUNFLOWER: Plasmophora halstedii, Scherotinia sclerotiorum, Aster Yellows, Septoria helianthi, Phomopsis helianthi, Alternaria helianthi, Alternaria zinniae, Botrytis cinera, Phoma macdonaldii, Macrophomina phaseolina, Erysiphe cichoracearum, Phizopus oryzae, Rhizopus arrhizus, Rhizopus stolonifer, Puccinia helianthi, Verticillium Dahliae, Erwinia carotovorum p.v. carotovora, Cephalosporium acremonium, Phytophthora cryptogea, Albugo tragopogonis.

SORGHUM: Exserohilum turcicum, Colletotrichum graminicola (Glomerella graminicola), Cercospora sorghi, Gloeocercospora sorghi, Ascochyta sorghi, Pseudomonas syringae p.v. syringae, Xanthomonas campestris p.v. holcicola, Pseudomonas andropogonis, Puccinia purpurea, Macrophomina phaseolina, Periconia circinata, Fusarium moniliforme, Alternaria alternate, Bipolaris sorghicola, Helminthosporium sorghicola, Curvularia lunata, Phoma insidiosa, Pseudomonas avenae (Pseudomonas alboprecipitans), Ramulispora sorghi, Ramulispora sorghicola, Phyllachara sacchari Sporisorium relianum (Sphacelotheca reliana), Sphacelotheca cruenta, Sporisorium sorghi, Sugarcane mosaic H, Maize Dwarf Mosaic Virus A & B, Claviceps sorghi, Rhizoctonia solani, Acremonium strictum, Sclerophthona macrospora, Peronosclerospora sorghi, Peronosclerospora philippinensis, Sclerospora graminicola, Fusarium graminearum, Fusarium Oxysporum, Pythium arrhenomanes, Pythium graminicola.

ALFALFA: Clavibater michiganensis subsp. Insidiosum, Pythium ultimum, Pythium irregulare, Pythium splendens, Pythium debaryanum, Pythium aphanidermatum, Phytophthora megasperma, Peronospora trifoliorum, Phoma medicaginis var. medicaginis, Cercospora medicaginis, Pseudopeziza medicaginis, Leptotrochila medicaginis, Fusarium oxysporum, Rhizoctonia solani, Uromyces striatus, Colletotrichum trifolii race 1 and race 2, Leptosphaerulina briosiana, Stemphylium botryosum, Stagonospora meliloti, Sclerotinia trifoliorum, Alfalfa Mosaic Virus, Verticillium albo-atrum, Xanthomonas campestris p.v. alfalfae, Aphanomyces euteiches, Stemphylium herbarum, Stemphylium alfalfae.

(v) Plant Agronomic Characteristics

Two of the factors determining where crop plants can be grown are the average daily temperature during the growing season and the length of time between frosts. Within the areas where it is possible to grow a particular crop, there are varying limitations on the maximal time it is allowed to grow to maturity and be harvested. For example, a variety to be grown in a particular area is selected for its ability to mature and dry down to harvestable moisture content within the required period of time with maximum possible yield. Therefore, crops of varying maturities are developed for different growing locations. Apart from the need to dry down sufficiently to permit harvest, it is desirable to have maximal drying take place in the field to minimize the amount of energy required for additional drying post harvest. Also, the more readily a product such as grain can dry down, the more time there is available for growth and kernel fill. It is considered that genes that influence maturity and/or dry down can be identified and introduced into plant lines using transformation techniques to create new varieties adapted to different growing locations or the same growing location, but having improved yield to moisture ratio at harvest. Expression of genes that are involved in regulation of plant development may be especially useful.

It is contemplated that genes may be introduced into plants that would improve standability and other plant growth characteristics. Expression of novel genes in plants which confer stronger stalks, improved root systems, or prevent or reduce ear droppage or shattering would be of great value to the farmer. It is proposed that introduction and expression of genes that increase the total amount of photoassimilate available by, for example, increasing light distribution and/or interception would be advantageous. In addition, the expression of genes that increase the efficiency of photosynthesis and/or the leaf canopy would further increase gains in productivity. It is contemplated that expression of a phytochrome gene in crop plants may be advantageous. Expression of such a gene may reduce apical dominance, confer semidwarfism on a plant, or increase shade tolerance (U.S. Pat. No. 5,268,526). Such approaches would allow for increased plant populations in the field.

(vi) Nutrient Utilization

The ability to utilize available nutrients may be a limiting factor in growth of crop plants. It is proposed that it would be possible to alter nutrient uptake, tolerate pH extremes, mobilization through the plant, storage pools, and availability for metabolic activities by the introduction of novel genes. These modifications would allow a plant, for example, maize to more efficiently utilize available nutrients. It is contemplated that an increase in the activity of, for example, an enzyme that is normally present in the plant and involved in nutrient utilization would increase the availability of a nutrient or decrease the availability of an antinutritive factor. An example of such an enzyme would be phytase. It is further contemplated that enhanced nitrogen utilization by a plant is desirable. Expression of a glutamate dehydrogenase gene in plants, e.g., E. coli gdhA genes, may lead to increased fixation of nitrogen in organic compounds. Furthermore, expression of gdhA in plants may lead to enhanced resistance to the herbicide glufosinate by incorporation of excess ammonia into glutamate, thereby detoxifying the ammonia. It also is contemplated that expression of a novel gene may make a nutrient source available that was previously not accessible, e.g., an enzyme that releases a component of nutrient value from a more complex molecule, perhaps a macromolecule.

Polypeptides useful for improving nitrogen flow, sensing, uptake, storage and/or transport include those involved in aspartate, glutamine or glutamate biosynthesis, polypeptides involved in aspartate, glutamine or glutamate transport, polypeptides associated with the TOR (Target of Rapamycin) pathway, nitrate transporters, nitrate reductases, amino transferases, ammonium transporters, chlorate transporters or polypeptides involved in tetrapyrrole biosynthesis.

Polypeptides useful for increasing the rate of photosynthesis include phytochrome, ribulose bisphosphate carboxylase-oxygenase, Rubisco activase, photosystem I and II proteins, electron carriers, ATP synthase, NADH dehydrogenase or cytochrome oxidase.

Polypeptides useful for increasing phosphorus uptake, transport or utilization include phosphatases or phosphate transporters.

(vii) Male Sterility

Male sterility is useful in the production of hybrid seed. It is proposed that male sterility may be produced through expression of novel genes. For example, it has been shown that expression of genes that encode proteins, RNAs, or peptides that interfere with development of the male inflorescence and/or gametophyte result in male sterility. Chimeric ribonuclease genes that express in the anthers of transgenic tobacco and oilseed rape have been demonstrated to lead to male sterility (Mariani et al., Nature, 347:737-741, 1990).

A number of mutations were discovered in maize that confer cytoplasmic male sterility. One mutation in particular, referred to as T cytoplasm, also correlates with sensitivity to Southern corn leaf blight. A DNA sequence, designated TURF 13 (Levings, Science, 250:942-947, 1990), was identified that correlates with T cytoplasm. It is proposed that it would be possible through the introduction of TURF 13 via transformation, to separate male sterility from disease sensitivity. As it is necessary to be able to restore male fertility for breeding purposes and for grain production, it is proposed that genes encoding restoration of male fertility also may be introduced.

(viii). Altered Nutritional Content

Genes may be introduced into plants to improve or alter the nutrient quality or content of a particular crop. Introduction of genes that alter the nutrient composition of a crop may greatly enhance the feed or food value. For example, the protein of many grains is suboptimal for feed and food purposes, especially when fed to pigs, poultry, and humans. The protein is deficient in several amino acids that are essential in the diet of these species, requiring the addition of supplements to the grain. Limiting essential amino acids may include lysine, methionine, tryptophan, threonine, valine, arginine, and histidine. Some amino acids become limiting only after corn is supplemented with other inputs for feed formulations. The levels of these essential amino acids in seeds and grain may be elevated by mechanisms which include, but are not limited to, the introduction of genes to increase the biosynthesis of the amino acids, decrease the degradation of the amino acids, increase the storage of the amino acids in proteins, or increase transport of the amino acids to the seeds or grain.

Polypeptides useful for providing increased seed protein quantity and/or quality include polypeptides involved in the metabolism of amino acids in plants, particularly polypeptides involved in biosynthesis of methionine/cysteine and lysine, amino acid transporters, amino acid efflux carriers, seed storage proteins, proteases, or polypeptides involved in phytic acid metabolism.

The protein composition of a crop may be altered to improve the balance of amino acids in a variety of ways including elevating expression of native proteins, decreasing expression of those with poor composition, changing the composition of native proteins, or introducing genes encoding entirely new proteins possessing superior composition.

The introduction of genes that alter the oil content of a crop plant may also be of value. Increases in oil content may result in increases in metabolizable-energy-content and density of the seeds for use in feed and food. The introduced genes may encode enzymes that remove or reduce rate-limitations or regulated steps in fatty acid or lipid biosynthesis. Such genes may include, but are not limited to, those that encode acetyl-CoA carboxylase, ACP-acyltransferase, alpha-ketoacyl-ACP synthase, or other well known fatty acid biosynthetic activities. Other possibilities are genes that encode proteins that do not possess enzymatic activity such as acyl carrier protein. Genes may be introduced that alter the balance of fatty acids present in the oil providing a more healthful or nutritive feedstuff. The introduced DNA also may encode sequences that block expression of enzymes involved in fatty acid biosynthesis, altering the proportions of fatty acids present in crops.

Genes may be introduced that enhance the nutritive value of crops, or of foods derived from crops by increasing the level of naturally occurring phytosterols, or by encoding for proteins to enable the synthesis of phytosterols in crops. The phytosterols from these crops can be processed directly into foods, or extracted and used to manufacture food products.

Genes may be introduced that enhance the nutritive value of the starch component of crops, for example by increasing the degree of branching, resulting in improved utilization of the starch in livestock by delaying its metabolism. Additionally, other major constituents of a crop may be altered, including genes that affect a variety of other nutritive, processing, or other quality aspects. For example, pigmentation may be increased or decreased.

Carbohydrate metabolism may be altered, for example by increased sucrose production and/or transport. Polypeptides useful for affecting on carbohydrate metabolism include polypeptides involved in sucrose or starch metabolism, carbon assimilation or carbohydrate transport, including, for example sucrose transporters or glucose/hexose transporters, enzymes involved in glycolysis/gluconeogenesis, the pentose phosphate cycle, or raffinose biosynthesis, or polypeptides involved in glucose signaling, such as SNF1 complex proteins.

Feed or food crops may also possess sub-optimal quantities of vitamins, antioxidants or other nutraceuticals, requiring supplementation to provide adequate nutritive value and ideal health value. Introduction of genes that enhance vitamin biosynthesis may be envisioned including, for example, vitamins A, E, B12, choline, or the like. Mineral content may also be sub-optimal. Thus genes that affect the accumulation or availability of compounds containing phosphorus, sulfur, calcium, manganese, zinc, or iron among others would be valuable.

Numerous other examples of improvements of crops may be used with the invention. The improvements may not necessarily involve grain, but may, for example, improve the value of a crop for silage. Introduction of DNA to accomplish this might include sequences that alter lignin production such as those that result in the “brown midrib” phenotype associated with superior feed value for cattle. Other genes may encode for enzymes that alter the structure of extracellular carbohydrates in the stover, or that facilitate the degradation of the carbohydrates in the non-grain portion of the crop so that it can be efficiently fermented into ethanol or other useful carbohydrates.

It may be desirable to modify the nutritional content of plants by reducing undesirable components such as fats, starches, etc. This may be done, for example, by the use of exogenous nucleic acids that encode enzymes which increase plant use or metabolism of such components so that they are present at lower quantities. Alternatively, it may be done by use of exogenous nucleic acids that reduce expression levels or activity of native plant enzymes that synthesize such components.

Likewise the elimination of certain undesirable traits may improve the food or feed value of the crop. Many undesirable traits must currently be eliminated by special post-harvest processing steps and the degree to which these can be engineered into the plant prior to harvest and processing would provide significant value. Examples of such traits are the elimination of anti-nutritionals such as phytates and phenolic compounds which are commonly found in many crop species. Also, the reduction of fats, carbohydrates and certain phytohormones may be valuable for the food and feed industries as they may allow a more efficient mechanism to meet specific dietary requirements.

In addition to direct improvements in feed or food value, genes also may be introduced which improve the processing of crops and improve the value of the products resulting from the processing. One use of crops is via wetmilling. Thus novel genes that increase the efficiency and reduce the cost of such processing, for example by decreasing steeping time, may also find use. Improving the value of wetmilling products may include altering the quantity or quality of starch, oil, corn gluten meal, or the components of gluten feed. Elevation of starch may be achieved through the identification and elimination of rate limiting steps in starch biosynthesis by expressing increased amounts of enzymes involved in biosynthesis or by decreasing levels of the other components of crops resulting in proportional increases in starch.

Oil is another product of wetmilling, the value of which may be improved by introduction and expression of genes. Oil properties may be altered to improve its performance in the production and use of cooking oil, shortenings, lubricants or other oil-derived products or improvement of its health attributes when used in the food-related applications. Novel fatty acids also may be synthesized which upon extraction can serve as starting materials for chemical syntheses. The changes in oil properties may be achieved by altering the type, level, or lipid arrangement of the fatty acids present in the oil. This in turn may be accomplished by the addition of genes that encode enzymes that catalyze the synthesis of novel fatty acids (e.g. fatty acid elongases, desaturases) and the lipids possessing them or by increasing levels of native fatty acids while possibly reducing levels of precursors or breakdown products. Alternatively, DNA sequences may be introduced which slow or block steps in fatty acid biosynthesis resulting in the increase in precursor fatty acid intermediates. Genes that might be added include desaturases, epoxidases, hydratases, dehydratases, or other enzymes that catalyze reactions involving fatty acid intermediates. Representative examples of catalytic steps that might be blocked include the desaturations from stearic to oleic acid or oleic to linolenic acid resulting in the respective accumulations of stearic and oleic acids. Another example is the blockage of elongation steps resulting in the accumulation of C8 to C12 saturated fatty acids.

Polypeptides useful for providing increased seed oil quantity and/or quality include polypeptides involved in fatty acid and glycerolipid biosynthesis, beta-oxidation enzymes, enzymes involved in biosynthesis of nutritional compounds, such as carotenoids and tocopherols, or polypeptides that increase embryo size or number or thickness of aleurone.

Polypeptides involved in production of galactomannans or arabinogalactans are of interest for providing plants having increased and/or modified reserve polysaccharides for use in food, pharmaceutical, cosmetic, paper and paint industries.

Polypeptides involved in modification of flavonoid/isoflavonoid metabolism in plants include cinnamate-4-hydroxylase, chalcone synthase or flavones synthase. Enhanced or reduced activity of such polypeptides in modified plants will provide changes in the quantity and/or speed of flavonoid metabolism in plants and may improve disease resistance by enhancing synthesis of protective secondary metabolites or improving signaling pathways governing disease resistance.

Polypeptides involved in lignin biosynthesis are of interest for increasing plants' resistance to lodging and for increasing the usefulness of plant materials as befouls.

(ix) Production or Assimilation of Chemicals or Biological

It may further be considered that a modified plant prepared in accordance with the invention may be used for the production or manufacturing of useful biological compounds that were either not produced at all, or not produced at the same level, in the corn plant previously. Alternatively, plants produced in accordance with the invention may be made to metabolize or absorb and concentrate certain compounds, such as hazardous wastes, thereby allowing bioremediation of these compounds.

The novel plants producing these compounds are made possible by the introduction and expression of one or potentially many genes with the constructs provided by the invention. The vast array of possibilities include but are not limited to any biological compound which is presently produced by any organism such as proteins, nucleic acids, primary and intermediary metabolites, carbohydrate polymers, enzymes for uses in bioremediation, enzymes for modifying pathways that produce secondary plant metabolites such as falconoid or vitamins, enzymes that could produce pharmaceuticals, and for introducing enzymes that could produce compounds of interest to the manufacturing industry such as specialty chemicals and plastics.

The compounds may be produced by the plant, extracted upon harvest and/or processing, and used for any presently recognized useful purpose such as pharmaceuticals, fragrances, and industrial enzymes to name a few.

(x) Other Characteristics

Cell cycle modification: Polypeptides encoding cell cycle enzymes and regulators of the cell cycle pathway are useful for manipulating growth rate in plants to provide early vigor and accelerated maturation. Improvements in quality traits, such as seed oil content, may also be obtained by expression of cell cycle enzymes and cell cycle regulators. Polypeptides of interest for modification of cell cycle pathway include cycling and EIF5alpha pathway proteins, polypeptides involved in polyamine metabolism, polypeptides which act as regulators of the cell cycle pathway, including cyclin-dependent kinases (CDKs), CDK-activating kinases, cell cycle-dependent phosphatases, CDK-inhibitors, Rb and Rb-binding proteins, or transcription factors that activate genes involved in cell proliferation and division, such as the E2F family of transcription factors, proteins involved in degradation of cyclins, such as cullins, and plant homologs of tumor suppressor polypeptides.

Plant growth regulators: Polypeptides involved in production of substances that regulate the growth of various plant tissues are of interest in the present invention and may be used to provide modified plants having altered morphologies and improved plant growth and development profiles leading to improvements in yield and stress response. Of particular interest are polypeptides involved in the biosynthesis, or degradation of plant growth hormones, such as gibberellins, brassinosteroids, cytokinins, auxins, ethylene or abscisic acid, and other proteins involved in the activity, uptake and/or transport of such polypeptides, including for example, cytokinin oxidase, cytokinin/purine permeases, F-box proteins, G-proteins or phytosulfokines.

Transcription factors in plants: Transcription factors play a key role in plant growth and development by controlling the expression of one or more genes in temporal, spatial and physiological specific patterns. Enhanced or reduced activity of such polypeptides in modified plants will provide significant changes in gene transcription patterns and provide a variety of beneficial effects in plant growth, development and response to environmental conditions. Transcription factors of interest include, but are not limited to myb transcription factors, including helix-turn-helix proteins, homeodomain transcription factors, leucine zipper transcription factors, MADS transcription factors, transcription factors having AP2 domains, zinc finger transcription factors, CCAAT binding transcription factors, ethylene responsive transcription factors, transcription initiation factors or UV damaged DNA binding proteins.

Homologous recombination: Increasing the rate of homologous recombination in plants is useful for accelerating the introgression of transgenes into breeding varieties by backcrossing, and to enhance the conventional breeding process by allowing rare recombinants between closely linked genes in phase repulsion to be identified more easily. Polypeptides useful for expression in plants to provide increased homologous recombination include polypeptides involved in mitosis and/or meiosis, DNA replication, nucleic acid metabolism, DNA repair pathways or homologous recombination pathways including for example, recombinases, nucleases, proteins binding to DNA double-strand breaks, single-strand DNA binding proteins, strand-exchange proteins, resolvases, ligases, helicases and polypeptide members of the RAD52 epistasis group.

Non-Protein-Expressing Exogenous Nucleic Acids

Plants with decreased expression of a gene of interest can also be achieved, for example, by expression of antisense nucleic acids, dsRNA or RNAi, catalytic RNA such as ribozymes, sense expression constructs that exhibit cosuppression effects, aptamers or zinc finger proteins.

Antisense RNA reduces production of the polypeptide product of the target messenger RNA, for example by blocking translation through formation of RNA:RNA duplexes or by inducing degradation of the target mRNA. Antisense approaches are a way of preventing or reducing gene function by targeting the genetic material as disclosed in U.S. Pat. Nos. 4,801,540; 5,107,065; 5,759,829; 5,910,444; 6,184,439; and 6,198,026, all of which are incorporated herein by reference. In one approach, an antisense gene sequence is introduced that is transcribed into antisense RNA that is complementary to the target mRNA. For example, part or all of the normal gene sequences are placed under a promoter in inverted orientation so that the ‘wrong’ or complementary strand is transcribed into a non-protein expressing antisense RNA. The promoter used for the antisense gene may influence the level, timing, tissue, specificity, or inducibility of the antisense inhibition.

Autonomous mini-chromosomes may contain exogenous DNA bounded by recombination sites, for example lox-P sites, that can be recognized by a recombinase, e.g. Cre, and removed from the mini-chromosome. In cases where there is a homologous recombination site or sites in the host genomic DNA, the exogenous DNA excised the mini-chromosome may be integrated into the genome at one of the specific recombination-sites and the DNA bounded by the recombination sites-will become integrated into the host DNA. The use of a mini-chromosome as a platform for DNA excision or for launching such DNA integration into the host genome may include in vivo induction of the expression of a recombinase encoded in the genomic DNA of a transgenic host, or in a mini-chromosome or other episome.

RNAi gene suppression in plants by transcription of a dsRNA is described in U.S. Pat. No. 6,506,559, U.S. patent application Publication No. 2002/0168707, WO 98/53083, WO 99/53050 and WO 99/61631, all of which are incorporated herein by reference. The double-stranded RNA or RNAi constructs can trigger the sequence-specific degradation of the target messenger RNA. Suppression of a gene by RNAi can be achieved using a recombinant DNA construct having a promoter operably linked to a DNA element comprising a sense and anti-sense element of a segment of genomic DNA of the gene, e.g., a segment of at least about 23 nucleotides, more preferably about 50 to 200 nucleotides where the sense and anti-sense DNA components can be directly linked or joined by an intron or artificial DNA segment that can form a loop when the transcribed RNA hybridizes to form a hairpin structure.

Catalytic RNA molecules or ribozymes can also be used to inhibit expression of the target gene or genes or facilitate molecular reactions. Ribozymes are targeted to a given sequence by hybridization of sequences within the ribozyme to the target mRNA. Two stretches of homology are required for this targeting, and these stretches of homologous sequences flank the catalytic ribozyme structure. It is possible to design ribozymes that specifically pair with virtually any target mRNA and cleave the target mRNA at a specific location, thereby inactivating it. A number of classes of ribozymes have been identified. One class of ribozymes is derived from a number of small circular RNAs that are capable of self-cleavage and replication in plants. The RNAs replicate either alone (viroid RNAs) or with a helper virus (satellite RNAs). Examples include Tobacco Ringspot Virus (Prody et al., Science, 231:1577-1580, 1986), Avocado Sunblotch Viroid (Palukaitis et al., Virology, 99:145-151, 1979; Symons, Nucl. Acids Res., 9:6527-6537, 1981), and Lucerne Transient Streak Virus (Forster and Symons, Cell, 49:211-220, 1987), and the satellite RNAs from velvet tobacco mottle virus, Solanum nodiflorum mottle virus and subterranean clover mottle virus. The design and use of target RNA-specific ribozymes is described in Haseloff, et al., Nature 334:585-591 (1988). Several different ribozyme motifs have been described with RNA cleavage activity (Symons, Annu. Rev. Biochem., 61:641-671, 1992). Other suitable ribozymes include sequences from RNase P with RNA cleavage activity (Yuan et al., Proc. Natl. Acad. Sci. USA, 89:8006-8010, 1992; Yuan and Altman, Science, 263:1269-1273, 1994; U.S. Pat. Nos. 5,168,053 and 5,624,824), hairpin ribozyme structures (Berzal-Herranz et al., Genes and Devel., 6:129-134, 1992; Chowrira et al., J. Biol. Chem., 269:25856-25864, 1994) and Hepatitis Delta virus based ribozymes (U.S. Pat. No. 5,625,047). The general design and optimization of ribozyme directed RNA cleavage activity has been discussed in detail (Haseloff and Gerlach, 1988, Nature. 1988 Aug. 18; 334(6183):585-91, Chowrira et al., J. Biol. Chem., 269:25856-25864, 1994).

Another method of reducing protein expression utilizes the phenomenon of cosuppression or gene silencing (for example, U.S. Pat. Nos. 6,063,947; 5,686,649; or 5,283,184; each of which is incorporated herein by reference). Cosuppression of an endogenous gene using a full-length cDNA sequence as well as a partial cDNA sequence are known (for example, Napoli et al., Plant Cell 2:279-289 [1990]; van der Krol et al., Plant Cell 2:291-299 [1990]; Smith et al., Mol. Gen. Genetics 224:477-481 [1990]). The phenomenon of cosuppression has also been used to inhibit plant target genes in a tissue-specific manner.

In some embodiments, nucleic acids from one species of plant are expressed in another species of plant to effect cosuppression of a homologous gene. The introduced sequence generally will be substantially identical to the endogenous sequence intended to be repressed, for example, about 65%, 80%, 85%, 90%, or preferably 95% or greater identical. Higher identity may result in a more effective repression of expression of the endogenous sequence. A higher identity in a shorter than full length sequence compensates for a longer, less identical sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and identity of non-coding segments will be equally effective. Generally, where inhibition of expression is desired, some transcription of the introduced sequence occurs. The effect may occur where the introduced sequence contains no coding sequence per se, but only intron or untranslated sequences homologous to sequences present in the primary transcript of the endogenous sequence.

Yet another method of reducing protein activity is by expressing nucleic acid ligands, so-called aptamers, which specifically bind to the protein. Aptamers may be obtained by the SELEX (Systematic Evolution of Ligands by EXponential Enrichment) method. See U.S. Pat. No. 5,270,163, incorporated herein by reference. In the SELEX method, a candidate mixture of single stranded nucleic acids having regions of randomized sequence is contacted with the protein and those nucleic acids having an increased affinity to the target are selected and amplified. After several iterations a nucleic acid with optimal affinity to the polypeptide is obtained and is used for expression in modified plants.

A zinc finger protein that binds a polypeptide-encoding sequence or its regulatory region is also used to alter expression of the nucleotide sequence. Transcription of the nucleotide sequence may be reduced or increased. Zinc finger proteins are, for example, described in Beerli et al. (1998) PNAS 95:14628-14633., or in WO 95/19431, WO 98/54311, or WO 96/06166, all incorporated herein by reference.

Other examples of non-protein expressing sequences specifically envisioned for use with the invention include tRNA sequences, for example, to alter codon usage, and rRNA variants, for example, which may confer resistance to various agents such as antibiotics.

It is contemplated that unexpressed DNA sequences, including novel synthetic sequences, could be introduced into cells as proprietary “labels” of those cells and plants and seeds thereof. It would not be necessary for a label DNA element to disrupt the function of a gene endogenous to the host organism, as the sole function of this DNA would be to identify the origin of the organism. For example, one could introduce a unique DNA sequence into a plant and this DNA element would identify all cells, plants, and progeny of these cells as having arisen from that labeled source. It is proposed that inclusion of label DNAs would enable one to distinguish proprietary germplasm or germplasm derived from such, from unlabelled germplasm.

Exemplary Plant Promoters, Regulatory Sequences and Targeting Sequences

Exemplary classes of plant promoters are described below.

Constitutive Expression promoters: Exemplary constitutive expression promoters include the ubiquitin promoter (e.g., sunflower—Binet et al. Plant Science 79: 87-94 (1991); maize—Christensen et al. Plant Molec. Biol. 12: 619-632 (1989); and Arabidopsis—Callis et al., J. Biol. Chem. 265: 12486-12493 (1990) and Norris et al., Plant Mol. Biol. 21: 895-906 (1993)); the CaMV 35S promoter (U.S. Pat. Nos. 5,858,742 and 5,322,938); or the actin promoter (e.g., rice—U.S. Pat. No. 5,641,876; McElroy et al. Plant Cell 2: 163-171 (1990), McElroy et al. Mol. Gen. Genet. 231: 150-160 (1991), and Chibbar et al. Plant Cell Rep. 12: 506-509 (1993)).

Inducible Expression promoters: Exemplary inducible expression promoters include the chemically regulatable tobacco PR-1 promoter (e.g., tobacco—U.S. Pat. No. 5,614,395; Arabidopsis—Lebel et al., Plant J. 16: 223-233 (1998); maize—U.S. Pat. No. 6,429,362). Various chemical regulators may be employed to induce expression, including the benzothiadiazole, isonicotinic acid, and salicylic acid compounds disclosed in U.S. Pat. Nos. 5,523,311 and 5,614,395. Other promoters inducible by certain alcohols or ketones, such as ethanol, include, for example, the alcA gene promoter from Aspergillus nidulans (Caddick et al. (1998) Nat. Biotechnol 16:177-180). A glucocorticoid-mediated induction system is described in Aoyama and Chua (1997) The Plant Journal 11: 605-612 wherein gene expression is induced by application of a glucocorticoid, for example a dexamethasone. Another class of useful promoters are water-deficit-inducible promoters, e.g. promoters which are derived from the 5′ regulatory region of genes identified as a heat shock protein 17.5 gene (HSP 17.5), an HVA22 gene (HVA22), and a cinnamic acid 4-hydroxylase (CA4H) gene (CA4H) of Zea maize. Another water-deficit-inducible promoter is derived from the rab-17 promoter as disclosed by Vilardell et al., Plant Molecular Biology, 17(5):985-993, 1990. See also U.S. Pat. No. 6,084,089 which discloses cold inducible promoters, U.S. Pat. No. 6,294,714 which discloses light inducible promoters, U.S. Pat. No. 6,140,078 which discloses salt inducible promoters, U.S. Pat. No. 6,252,138 which discloses pathogen inducible promoters, and U.S. Pat. No. 6,175,060 which discloses phosphorus deficiency inducible promoters.

As another example, numerous wound-inducible promoters have been described (e.g. Xu et al. Plant Molec. Biol. 22: 573-588 (1993), Logemann et al. Plant Cell 1: 151-158 (1989), Rohrmeier & Lehle, Plant Molec. Biol. 22: 783-792 (1993), Firek et al. Plant Molec. Biol. 22: 129-142 (1993), Warner et al. Plant J. 3: 191-201 (1993)). Logemann describe 5′ upstream sequences of the potato wunl gene. Xu et al. show that a wound-inducible promoter from the dicotyledon potato (pin2) is active in the monocotyledon rice. Rohrmeier & Lehle describe maize Wipl cDNA which is wound induced and which can be used to isolate the cognate promoter. Firek et al. and Warner et al. have described a wound-induced gene from the monocotyledon Asparagus officinalis, which is expressed at local wound and pathogen invasion sites.

Tissue-Specific Promoters: Exemplary promoters that express genes only in certain tissues are useful according to the present invention. For example root specific expression may be attained using the promoter of the maize metallothionein-like (MTL) gene described by de Framond (FEBS 290: 103-106 (1991)) and also in U.S. Pat. No. 5,466,785, incorporated herein by reference. U.S. Pat. No. 5,837,848 discloses a root specific promoter. Another exemplary promoter confers pith-preferred expression (see Int'l. Pub. No. WO 93/07278, herein incorporated by reference, which describes the maize trpA gene and promoter that is preferentially expressed in pith cells). Leaf-specific expression may be attained, for example, by using the promoter for a maize gene encoding phosphoenol carboxylase (PEPC) (see Hudspeth & Grula, Plant Molec Biol 12: 579-589 (1989)). Pollen-specific expression may be conferred by the promoter for the maize calcium-dependent protein kinase (CDPK) gene which is expressed in pollen cells (WO 93/07278). U.S. Pat. Appl. Pub. No. 20040016025 describes tissue-specific promoters. Pollen-specific expression may be conferred by the tomato LAT52 pollen-specific promoter (Bate et. al., Plan mol Biol. 1998 July; 37(5):859-69).

See also U.S. Pat. No. 6,437,217 which discloses a root-specific maize RS81 promoter, U.S. Pat. No. 6,426,446 which discloses a root specific maize RS324 promoter, U.S. Pat. No. 6,232,526 which discloses a constitutive maize A3 promoter, U.S. Pat. No. 6,177,611 which discloses constitutive maize promoters, U.S. Pat. No. 6,433,252 which discloses a maize L3 oleosin promoter that are aleurone and seed coat-specific promoters, U.S. Pat. No. 6,429,357 which discloses a constitutive rice actin 2 promoter and intron, U.S. patent application Pub. No. 20040216189 which discloses an inducible constitutive leaf specific maize chloroplast aldolase promoter.

Optionally a plant transcriptional terminator can be used in place of the plant-expressed gene native transcriptional terminator. Exemplary transcriptional terminators are those that are known to function in plants and include the CaMV 35S terminator, the tml terminator, the nopaline synthase terminator and the pea rbcS E9 terminator. These can be used in both monocotyledons and dicotyledons.

Various intron sequences have been shown to enhance expression, particularly in monocotyledonous cells. For example, the introns of the maize Adh1 gene have been found to significantly enhance expression. Intron 1 was found to be particularly effective and enhanced expression in fusion constructs with the chloramphenicol acetyltransferase gene (Callis et al., Genes Develop. 1: 1183-1200 (1987)). The intron from the maize bronzel gene also enhances expression. Intron sequences have been routinely incorporated into plant transformation vectors, typically within the non-translated leader. U.S. Patent Application Publication 2002/0192813 discloses 5′, 3′ and intron elements useful in the design of effective plant expression vectors.

A number of non-translated leader sequences derived from viruses are also known to enhance expression, and these are particularly effective in dicotyledonous cells. Specifically, leader sequences from Tobacco Mosaic Virus (TMV, the “omega-sequence”), Maize Chlorotic Mottle Virus (MCMV), and Alfalfa Mosaic Virus (AMV) have been shown to be effective in enhancing expression (e.g: Gallie et al. Nucl. Acids Res. 15: 8693-8711 (1987); Skuzeski et al. Plant Molec. Biol. 15: 65-79 (1990)). Other leader sequences known in the art include but are not limited to: picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein, O., Fuerst, T. R., and Moss, B. PNAS USA 86:6126-6130 (1989)); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Allison et al., 1986); MDMV leader (Maize Dwarf Mosaic Virus); Virology 154:9-20); human immunoglobulin heavy-chain binding protein (BiP) leader, (Macejak, D. G., and Sarnow, P., Nature 353: 90-94 (1991); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4), (Jobling, S. A., and Gehrke, L., Nature 325:622-625 (1987); tobacco mosaic virus leader (TMV), (Gallie et al., Molecular Biology of RNA, pages 237-256 (1989); or Maize Chlorotic Mottle Virus leader (MCMV) (Lommel et al., Virology 81:382-385 (1991). See also, Della-Cioppa et al., Plant Physiology 84:965-968 (1987).

A minimal promoter may also be incorporated. Such a promoter has low background activity in plants when there is no transactivator present or when enhancer or response element binding sites are absent. One exemplary minimal promoter is the Bz1 minimal promoter, which is obtained from the bronzel gene of maize. Roth et al., Plant Cell 3: 317 (1991). A minimal promoter may also be created by use of a synthetic TATA element. The TATA element allows recognition of the promoter by RNA polymerase factors and confers a basal level of gene expression in the absence of activation (see generally, Mukumoto (1993) Plant Mol Biol 23: 995-1003; Green (2000) Trends Biochem Sci 25: 59-63).

Sequences controlling the targeting of gene products also may be included. For example, the targeting of gene products to the chloroplast is controlled by a signal sequence found at the amino terminal end of various proteins which is cleaved during chloroplast import to yield the mature protein (e.g. Comai et al. J. Biol. Chem. 263: 15104-15109 (1988)). These signal sequences can be fused to heterologous gene products to effect the import of heterologous products into the chloroplast (van den Broeck, et al. Nature 313: 358-363 (1985)). DNA encoding for appropriate signal sequences can be isolated from the 5′ end of the cDNAs encoding the RUBISCO protein, the CAB protein, the EPSP synthase enzyme, the GS2 protein or many other proteins which are known to be chloroplast localized. Other gene products are localized to other organelles such as the mitochondrion and the peroxisome (e.g. Unger et al. Plant Molec. Biol. 13: 411-418 (1989)). Examples of sequences that target to such organelles are the nuclear-encoded ATPases or specific aspartate amino transferase isoforms for mitochondria. Targeting cellular protein bodies has been described by Rogers et al. (Proc. Natl. Acad. Sci. USA 82: 6512-6516 (1985)). In addition, amino terminal and carboxy-terminal sequences are responsible for targeting to the ER, the apoplast, and extracellular secretion from aleurone cells (Koehler & Ho, Plant Cell 2: 769-783 (1990)). Additionally, amino terminal sequences in conjunction with carboxy terminal sequences are responsible for vacuolar targeting of gene products (Shinshi et al. Plant Molec. Biol. 14: 357-368 (1990)).

Another possible element which may be introduced is a matrix attachment region element (MAR), such as the chicken lysozyme A element (Stief, 1989), which can be positioned around an expressible gene of interest to effect an increase in overall expression of the gene and diminish position dependent effects upon incorporation into the plant genome (Stief et al., Nature, 341:343, 1989; Phi-Van et al., Mol. Cell. Biol., 10:2302-2307.1990).

Use of Non-Plant Promoter Regions Isolated from Drosophila Melanogaster and Saccharomyces Cerevisiae to Express Genes in Plants

The promoter in the mini-chromosome of the present invention can be derived from plant or non-plant species. In a preferred embodiment, the nucleotide sequence of the promoter is derived from non-plant species for the expression of genes in plant cells, including but not limited to dicotyledon plant cells such as tobacco, tomato, potato, soybean, canola, sunflower, alfalfa, cotton and Arabidopsis, or monocotyledonous plant cell, such as wheat, maize, rye, rice, turf grass, oat, barley, sorghum, millet, and sugarcane. In one embodiment, the non-plant promoters are constitutive or inducible promoters derived from insect, e.g., Drosophila melanogaster or yeast, e.g., Saccharomyces cerevisiae. Table 2 lists the promoters from Drosophila melanogaster and Saccharomyces cerevisiae that are used to derive the examples of non-plant promoters in the present invention. Promoters derived from any animal, protist, or fungi are also contemplated. SEQ ID NOS: 4-23 are examples of promoter sequences derived from Drosophila melanogaster or Saccharomyces cerevisiae. These non-plant promoters can be operably-linked to nucleic acid sequences encoding polypeptides or non-protein-expressing sequences including, but not limited to, antisense RNA and ribozymes, to form nucleic acid constructs, vectors, and host cells (prokaryotic or eukaryotic), comprising the promoters.

TABLE 2 Drosophila melanogaster Promoters (adapted from the Drosophila FlyBase, referenced in Grumbling, G. and Strelets, V. FlyBase: anatomical data, images and queries. Nucl. Acids Rsrch. 34: D484-8. Standard promoter gene Seq Id No. Symbol Flybase ID name Gene Product Chromosome  4 gd FBgn0004654 Phosphogluconate 6- X dehydrogenase phosphogluconate dehydrogenase  5 rim FBgn0015946 grim grim-P138 3  5 ro FBgn0003961 Urate oxidase Uro-P1 2  7 na FBgn0003448 snail sna-P1 2  8 h3 FBgn0003249 Rhodopsin 3 Rh3 3  9 sp-1 γ FBgn0002564 Larval serum Lsp1γ-PI 3 protein 1 γ Saccharomyces cerevisiae Promoters (adapted from information available from the Saccharomyces Genome Database, referenced in Dwight S S, Balakrishnan R, Christie K R, et al. 2004. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 5: 9-22). Standard Seq Systematic promoter gene Id No. Symbol Name name Gene Product Chromosome 10 ef-2 YBR118W TEF2 Translation 2 (Translation elongation factor elongation factor EF-1 alpha promoter) 11 eu-1 YGL009C LEU1 (LEUcine isopropylmalate 7 biosynthesis) isomerase 12 et16 YPR167C METhionine 3′phosphoadenylyl- 16 requiring sulfate reductase 13 eu-2 YCL018W LEU2 (leucine beta-IPM 3 biosynthesis) (isopropylmalate) dehydrogenase 14 is-4 YCL030C HIS4 (HIStidine histidinol 3 requiring) dehydrogenase 15 et-2 YNL277W MET2 L-homoserine-O- 14 (methionine acetyltransferase requiring) 16 te-3 YKL178C STE3 (alias a-factor receptor 11 DAF2 Sterile) 17 rg-1 YOL058W ARG1 (alias arginosuccinate 15 ARG10 synthetase ARGinine requiring) 18 gk-1 YCR012W PGK1 phosphoglycerate 3 (phosphoglycerate kinase kinase) 19 PD-1 YDL022W GPD1 (alias glycerol-3- 4 DAR1/HOR1/OSG1/ phosphate OSR5: dehydrogenase glycerol-3- phosphate dehydrogenase activity 20 DH1 YOL086C ADH1 (alias alcohol 15 ADC1) dehydrogenase 21 PD-2 YOL059W GPD2 (alias glycerol-3- 15 GPD3: glycerol- phosphate 3-phosphate dehydrogenase dehydrogenase activity 22 rg-4 YHR018C ARGinine argininosuccinate 8 requiring lyase 23 at-1 YAR035W YAT-1 (carnitine carnitine 1 acetyltransferase) acetyltransferase

The present invention relates to methods for producing a polypeptide, comprising cultivating plant material for the production of the polypeptide at any level, wherein the plant host cells comprises a first nucleic acid sequence encoding the polypeptide operably linked to a second nucleic acid sequence comprising a heterologous promoter foreign to the nucleic acid sequence, wherein the promoter comprises a sequence selected from the group consisting of SEQ ID NOS:4 to 23 or subsequences thereof; and mutant, hybrid, or tandem promoters thereof that retain promoter activity.

The present invention also relates to methods for producing non-protein expressed sequences, comprising cultivating plant material for the production of the non-protein expressed sequence, wherein the plant host cell comprises a first nucleic acid sequence encoding the non-protein expressed sequences operably linked to a second nucleic acid sequence comprising a heterologous promoter foreign to the nucleic acid sequence, wherein the promoter comprises a sequence selected from the group consisting of SEQ ID NOS:4 to 23 or subsequences thereof; and mutant, hybrid, or tandem promoters thereof.

The present invention also relates to isolated promoter sequences and to constructs, vectors, or plant host cells comprising one or more of the promoters operably linked to a nucleic acid sequence encoding a polypeptide or non-protein expressing sequence.

In the methods of the present invention, the promoter may also be a mutant of the promoters having a substitution, deletion, and/or insertion of one or more nucleotides in the nucleic acid sequence of SEQ ID NOS:4 to 23.

The present invention also relates to methods for obtaining derivative promoters of SEQ ID NOS:4 to 23.

The techniques used to isolate or clone a nucleic acid sequence comprising a promoter of interest are known in the art and include isolation from genomic DNA. The cloning procedures may involve excision or amplification, for example by polymerase chain reaction, and isolation of a desired nucleic acid fragment comprising the nucleic acid sequence encoding the promoter, insertion of the fragment into a vector molecule, and incorporation of the recombinant vector into the plant cell.

Definitions

The term “adchromosomal” plant or plant part, as used herein means a plant or plant part that contains functional, stable and autonomous mini-chromosomes. Adchromosomal plants or plant parts may be chimeric or not chimeric (chimeric meaning that mini-chromosomes are only in certain portions of the plant, and are not uniformly distributed throughout the plant). An adchromosomal plant cell contains at least one functional, stable and autonomous mini-chromosome.

The term “autonomous” as used herein means that when delivered to plant cells, at least some mini-chromosomes are transmitted through mitotic division to daughter cells and are episomal in the daughter plant cells, i.e. are not chromosomally integrated in the daughter plant cells. Daughter plant cells that contain autonomous mini-chromosomes can be selected for further replication using, for example, selectable or screenable markers. During the introduction into a cell of a mini-chromosome, or during subsequent stages of the cell cycle, there may be chromosomal integration of some portion or all of the DNA derived from a mini-chromosome in some cells. The mini-chromosome is still characterized as autonomous despite the occurrence of such events if a plant may be regenerated that contains episomal descendants of the mini-chromosome distributed throughout its parts, or if gametes or progeny can be derived from the plant that contain episomal descendants of the mini-chromosome distributed through its parts.

As used herein, a “centromere” is any DNA sequence that confers an ability to segregate to daughter cells through cell division. In one context, this sequence may produce a transmission efficiency to daughter cells ranging from about 1% to about 100%, including to about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or about 95% of daughter cells. Variations in such a transmission efficiency may find important applications within the scope of the invention; for example, mini-chromosomes carrying centromeres that confer 100% stability could be maintained in all daughter cells without selection, while those that confer 1% stability could be temporarily introduced into a transgenic organism, but be eliminated when desired. In particular embodiments of the invention, the centromere may confer stable transmission to daughter cells of a nucleic acid sequence, including a recombinant construct comprising the centromere, through mitotic or meiotic divisions, including through both meiotic and meiotic divisions. A plant centromere is not necessarily derived from plants, but has the ability to promote DNA transmission to daughter plant cells.

As used herein, the term “circular permutations” refer to variants of a sequence that begin at base n within the sequence, proceed to the end of the sequence, resume with base number one of the sequence, and proceed to base n−1. For this analysis, n may be any number less than or equal to the length of the sequence. For example, circular permutations of the sequence ABCD are: ABCD, BCDA, CDAB, and DABC.

The term “co-delivery” as used herein refers to the delivery of two nucleic acid segments to a cell. In co-delivery of plant growth inducing genes and mini-chromosomes, the two nucleic acid segments are delivered simultaneously using the same delivery method. Alternatively, the nucleic acid segment containing the growth inducing gene, optionally as part of an episomal vector, such as a viral vector or a plasmid vector, may be delivered to the plant cells before or after delivery of the mini-chromosome, and the mini-chromosome may carry an exogenous nucleic acid that induces expression of the earlier-delivered growth inducing gene. In this embodiment, the two nucleic acid segments may be delivered separately at different times provided the encoded growth inducing factors are functional during the appropriate time period.

The term “coding sequence” is defined herein as a nucleic acid sequence that is transcribed into mRNA which is translated into a polypeptide when placed under the control of promoter sequences. The boundaries of the coding sequence are generally determined by the ATG start codon located at the start of the open reading frame, near the 5′ end of the mRNA, and TAG, TGA or TAA stop codons at the end of the coding sequence, near the 3′ end f the mRNA, and in some cases, a transcription terminator sequence located just downstream of the open reading frame at the 3′ end of the mRNA. A coding sequence can include, but is not limited to, genomic DNA, cDNA, semisynthetic, synthetic, or recombinant nucleic acid sequences.

As used herein the term “consensus” refers to a nucleic acid sequence derived by comparing two or more related sequences. A consensus sequence defines both the conserved and variable sites between the sequences being compared. Any one of the sequences used to derive the consensus or any permutation defined by the consensus may be useful in construction of mini-chromosomes.

The term “exogenous” when used in reference to a nucleic acid, for example, is intended to refer to any nucleic acid that has been introduced into a recipient cell, regardless of whether the same or similar nucleic acid is already present in such a cell. Thus, as an example, “exogenous DNA” can include an additional copy of DNA that is already present in the plant cell, DNA from another plant, DNA from a different organism, or a DNA generated externally, such as a DNA sequence containing an antisense message of a gene, or a DNA sequence encoding a synthetic or modified version of a gene. An “exogenous gene” can be a gene not normally found in the host genome in an identical context, or an extra copy of a host gene. The gene may be isolated from a different species than that of the host genome, or alternatively, isolated from the host genome but operably linked to one or more regulatory regions which differ from those found in the unaltered, native gene.

The term “functional” as used herein to describe a mini-chromosome means that when an exogenous nucleic acid is present within the mini-chromosome the exogenous nucleic acid can function in a detectable manner when the mini-chromosome is within a plant cell; exemplary functions of the exogenous nucleic acid include transcription of the exogenous nucleic acid, expression of the exogenous nucleic acid, regulatory control of expression of other exogenous nucleic acids, recognition by a restriction enzyme or other endonuclease, ribozyme or recombinase; providing a substrate for DNA methylation, DNA glycolation or other DNA chemical modification; binding to proteins such as histones, helix-loop-helix proteins, zinc binding proteins, leucine zipper proteins, MADS box proteins, topoisomerases, helicases, transposases, TATA box binding proteins, viral protein, reverse transcriptases, or cohesins; providing an integration site for homologous recombination; providing an integration site for a transposon, T-DNA or retrovirus; providing a substrate for RNAi synthesis; priming of DNA replication; aptamer binding; or kinetochore binding. if multiple exogenous nucleic acids are present within the mini-chromosome, the function of one or preferably more of the exogenous nucleic acids can be detected under suitable conditions permitting function thereof.

As used herein, a “library” is a pool of cloned DNA fragments that represents some or all DNA sequences collected, prepared or purified from a specific source. Each library may contain the DNA of a given organism inserted as discrete restriction enzyme generated fragments or as randomly sheared fragments into many thousands of plasmid vectors. For purposes of the present invention, E. coli, yeast, and Salmonella plasmids are particularly useful for propagating the genome inserts from other organisms. In principle, any gene or sequence present in the starting DNA preparation can be isolated by screening the library with a specific hybridization probe (see, for example, Young et al., In: Eukaryotic Genetic Systems ICN-UCLA Symposia on Molecular and Cellular Biology, VII, 315-331, 1977).

As used herein, the term “linker” refers to a DNA molecule, generally up to 50 or 60 nucleotides long and composed of two or more complementary oligonucleotides that have been synthesized chemically, or excised or amplified from existing plasmids or vectors. In a preferred embodiment, this fragment contains one, or preferably more than one, restriction enzyme site for a blunt cutting enzyme and/or a staggered cutting enzyme, such as BamHI. One end of the linker is designed to be ligatable to one end of a linear DNA molecule and the other end is designed to be ligatable to the other end of the linear molecule, or both ends may be designed to be ligatable to both ends of the linear DNA molecule.

As used herein, a “mini-chromosome” is a recombinant DNA construct including a centromere and capable of transmission to daughter cells. A mini-chromosome may remain separate from the host genome (as episomes) or may integrate into host chromosomes. The stability of this construct through cell division could range between from about 1% to about 100%, including about 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% and about 95%. The mini-chromosome construct may be a circular or linear molecule. It may include elements such as one or more telomeres, origin of replication sequences, stuffer sequences, buffer sequences, chromatin packaging sequences, linkers and genes. The number of such sequences included is only limited by the physical size limitations of the construct itself. It could contain DNA derived from a natural centromere, although it may be preferable to limit the amount of DNA to the minimal amount required to obtain a transmission efficiency in the range of 1-100%. The mini-chromosome could also contain a synthetic centromere composed of tandem arrays of repeats of any sequence, either derived from a natural centromere, or of synthetic DNA. The mini-chromosome could also contain DNA derived from multiple natural centromeres. The mini-chromosome may be inherited through mitosis or meiosis, or through both meiosis and mitosis. As used herein, the term mini-chromosome specifically encompasses and includes the terms “plant artificial chromosome” or “PLAC,” or engineered chromosomes or microchromosomes and all teachings relevant to a PLAC or plant artificial chromosome specifically apply to constructs within the meaning of the term mini-chromosome.

The term “non-protein expressing sequence” or “non-protein coding sequence” is defined herein as a nucleic acid sequence that is not eventually translated into protein. The nucleic acid may or may not be transcribed into RNA. Exemplary sequences include ribozymes or antisense RNA.

The term “operably linked” is defined herein as a configuration in which a control sequence, e.g., a promoter sequence, directs transcription or translation of another sequence, for example a coding sequence. For example, a promoter sequence could be appropriately placed at a position relative to a coding sequence such that the control sequence directs the production of a polypeptide encoded by the coding sequence.

“Phenotype” or “phenotypic trait(s)”, as used herein, refers to an observable property or set of properties resulting from the expression of a gene. The set of properties may be observed visually or after biological or biochemical testing, and may be constantly present or may only manifest upon challenge with the appropriate stimulus or activation with the appropriate signal.

The term “plant,” as used herein, refers to any type of plant. Exemplary types of plants are listed below, but other types of plants will be known to those of skill in the art and could be used with the invention. Modified plants of the invention include, for example, dicots, gymnosperm, monocots, mosses, ferns, horsetails, club mosses, liver worts, hornworts, red algae, brown algae, gametophytes and sporophytes of pteridophytes, and green algae.

The term “crop plant” refers to plants grown for agricultural or commercial rather than experimental purposes and specifically excludes Arabidopsis thaliana. Some plants grown for experimental purposes may take on commercial importance when used to produce pharmaceutical or chemical products. Centromeres “derived from crop plants” according to the present invention specifically exclude centromeres that are fragments of naturally occurring Arabidopsis thaliana centromeres or naturally occurring descendants thereof. Centromeres derived from crop plants include variants (mutants) of Arabidopsis thaliana centromeres, or artificial centromeres synthesized based on nucleotide sequences of Arabidopsis thaliana centromeres.

A common class of plants exploited in agriculture are vegetable crops, including artichokes, kohlrabi, arugula, leeks, asparagus, lettuce (e.g., head, leaf, romaine), bok choy, malanga, broccoli, melons (e.g., muskmelon, watermelon, crenshaw, honeydew, cantaloupe), brussels sprouts, cabbage, cardoni, carrots, napa, cauliflower, okra, onions, celery, parsley, chick peas, parsnips, chicory, chinese cabbage, peppers, collards, potatoes, cucumber plants (marrows, cucumbers), pumpkins, cucurbits, radishes, dry bulb onions, rutabaga, eggplant, salsify, escarole, shallots, endive, garlic, spinach, green onions, squash, greens, beet (sugar beet or fodder beet), sweet potatoes, swiss chard, horseradish, tomatoes, kale, turnips, or spices.

Other types of plants frequently finding commercial use include fruit and vine crops such as apples, grapes, apricots, cherries, nectarines, peaches, pears, plums, prunes, quince, almonds, chestnuts, filberts, pecans, pistachios, walnuts, citrus, blueberries, boysenberries, cranberries, currants, loganberries, raspberries, strawberries, blackberries, grapes, avocados, bananas, kiwi, persimmons, pomegranate, pineapple, tropical fruits, pomes, melon, mango, papaya, or lychee.

Modified wood and fiber or pulp plants of particular interest include, but are not limited to maple, oak, cherry, mahogany, poplar, aspen, birch, beech, spruce, fir, kenaf, pine, walnut, cedar, redwood, chestnut, acacia, bombax, alder, eucalyptus, catalpa, mulberry, persimmon, ash, honeylocust, sweetgum, privet, sycamore, magnolia, sourwood, cottonwood, mesquite, buckthorn, locust, willow, elderberry, teak, linden, bubing a, basswood or elm.

Modified flowers and ornamental plants of particular interest, include, but are not limited to, roses, petunias, pansy, peony, olive, begonias, violets, phlox, nasturtiums, irises, lilies, orchids, vinca, philodendron, poinsettias, opuntia, cyclamen, magnolia, dogwood, azalea, redbud, boxwood, Viburnum, maple, elderberry, hosta, agave, asters, sunflower, pansies, hibiscus, morning glory, alstromeria, zinnia, geranium, Prosopis, artemesia, clematis, delphinium, dianthus, gallium, coreopsis, iberis, lamium, poppy, lavender, leucophyllum, sedum, salvia, verbascum, digitalis, penstemon, savory, pythrethrum, or oenothera. Modified nut-bearing trees of particular interest include, but are not limited to pecans, walnuts, macadamia nuts, hazelnuts, almonds, or pistachios, cashews, pignolas or chestnuts.

Many of the most widely grown plants are field crop plants such as evening primrose, meadow foam, corn (field, sweet, popcorn), hops, jojoba, peanuts, rice, safflower, small grains (barley, oats, rye, wheat, etc.), sorghum, tobacco, kapok, leguminous plants (beans, lentils, peas, soybeans), oil plants (rape, mustard, poppy, olives, sunflowers, coconut, castor oil plants, cocoa beans, groundnuts, oil palms), fibre plants (cotton, flax, hemp, jute), lauraceae (cinnamon, camphor), or plants such as coffee, sugarcane, cocoa, tea, or natural rubber plants. Still other examples of plants include bedding plants such as flowers, cactus, succulents or ornamental plants, as well as trees such as forest (broad-leaved trees or evergreens, such as conifers), fruit, ornamental, or nut-bearing trees, as well as shrubs or other nursery stock.

Still other examples of plants include bedding plants such as flowers, cactus, succulents or ornamental plants, as well as trees such as forest (broad-leaved trees or evergreens, such as conifers), fruit, ornamental, or nut-bearing trees, as well as shrubs or other nursery stock.

Modified crop plants of particular interest in the present invention include, but are not limited to, soybean (including the variety known as Glycine max), cotton, canola (also known as rape), wheat, sunflower, sorghum, alfalfa, barley, safflower, millet, rice, tobacco, fruit and vegetable crops or turfgrasses. Exemplary cereals include maize, wheat, barley, oats, rye, millet, sorghum, rice triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum sp., or teosinte. Oil-producing plants include plant species that produce and store triacylglycerol in specific organs, primarily in seeds. Such species include soybean (Glycine max), rapeseed or canola (including Brassica napus, Brassica rapa or Brassica campestris), Brassica juncea, Brassica carinata, sunflower (Helianthus annus), cotton (Gossypium hirsutum), corn (Zea mays), cocoa (Theobroma cacao), safflower (Carthamus tinctorius), oil palm (Elaeis guineensis), coconut palm (Cocos nucifera), flax (Linum usitatissimum), castor (Ricinus communis) or peanut (Arachis hypogaea).

The term “plant part” as used herein includes pollen, silk, endosperm, ovule, seed, embryo, pods, roots, cuttings, tubers, stems, stalks, fruit, berries, nuts, flowers, leaves, bark, wood, whole plant, plant cell, plant organ, protoplast, cell culture, crown, callus culture, petiole, petal, sepal, stamen, stigma, style, bud, or any group of plant cells organized into a structural and functional unit. In one preferred embodiment, the exogenous nucleic acid is expressed in a specific location or tissue of a plant, for example, epidermis, vascular tissue, meristem, cambium, cortex, pith, leaf, sheath, flower, root or seed.

The term “promoter” is defined herein as a DNA sequence that allows the binding of RNA polymerase (including but not limited to RNA polymerase I, RNA polymerase II and RNA polymerase III from eukaryotes) and directs the polymerase to a downstream transcriptional start site of a nucleic acid sequence encoding a polypeptide to initiate transcription. RNA polymerase effectively catalyzes the assembly of messenger RNA complementary to the appropriate DNA strand of the coding region.

A “promoter operably linked to a heterologous gene” is a promoter that is operably linked to a gene that is different from the gene to which the promoter is normally operably linked in its native state. Similarly, an “exogenous nucleic acid operably linked to a heterologous regulatory sequence” is a nucleic acid that is operably linked to a regulatory control sequence to which it is not normally linked in its native state.

The term “hybrid promoter” is defined herein as parts of two or more promoters that are fused together to generate a sequence that is a fusion of the two or more promoters, which is operably linked to a coding sequence and mediates the transcription of the coding sequence into mRNA.

The term “tandem promoter” is defined herein as two or more promoter sequences each of which is operably linked to a coding sequence and mediates the transcription of the coding sequence into mRNA.

The term “constitutive active promoter” is defined herein as a promoter that allows permanent stable expression of the gene of interest.

The term “Inducible promoter” is defined herein as a promoter induced by the presence or absence of biotic or an abiotic factor.

The term “polypeptide” does not refer to a specific length of the encoded product and, therefore, encompasses peptides, oligopeptides, and proteins. The term “exogenous polypeptide” is defined as a polypeptide which is not native to the plant cell, a native polypeptide in which modifications have been made to alter the native sequence, or a native polypeptide whose expression is quantitatively altered as a result of a manipulation of the plant cell by recombinant DNA techniques.

As used herein, the term “pseudogene” refers to a non-functional copy of a protein-coding gene; pseudogenes found in the genomes of eukaryotic organisms are often inactivated by mutations and are thus presumed to be non-essential to that organism; pseudogenes of reverse transcriptase and other open reading frames found in retroelements are abundant in the centromeric regions of Arabidopsis and other organisms and are often present in complex clusters of related sequences.

As used herein the term “regulatory sequence” refers to any DNA sequence that influences the efficiency of transcription or translation of any gene. The term includes, but is not limited to, sequences comprising promoters, enhancers and terminators.

As used herein the term “repeated nucleotide sequence” refers to any nucleic acid sequence of at least 25 bp present in a genome or a recombinant molecule, other than a telomere repeat, that occurs at least two or more times and that are preferably at least 80% identical either in head to tail or head to head orientation either with or without intervening sequence between repeat units.

As used herein, the term “retroelement” or “retrotransposon” refers to a genetic element related to retroviruses that disperse through an RNA stage; the abundant retroelements present in plant genomes contain long terminal repeats (LTR retrotransposons) and encode a polyprotein gene that is processed into several proteins including a reverse transcriptase. Specific retroelements (complete or partial sequences) can be found in and around plant centromeres and can be present as dispersed copies or complex repeat clusters. Individual copies of retroelements may be truncated or contain mutations; intact retrolements are rarely encountered.

As used herein the term “satellite DNA” refers to short DNA sequences (typically <1000 bp) present in a genome as multiple repeats, mostly arranged in a tandemly repeated fashion, as opposed to a dispersed fashion. Repetitive arrays of specific satellite repeats are abundant in the centromeres of many higher eukaryotic organisms.

As used herein, a “screenable marker” is a gene whose presence results in an identifiable phenotype. This phenotype may be observable under standard conditions, altered conditions such as elevated temperature, or in the presence of certain chemicals used to detect the phenotype. The use of a screenable marker allows for the use of lower, sub-killing antibiotic concentrations and the use of a visible marker gene to identify clusters of transformed cells, and then manipulation of these cells to homogeneity. Preferred screenable markers of the present include genes that encode fluorescent proteins that are detectable by a visual microscope such as the fluorescent reporter genes DsRed, ZsGreen, ZsYellow, AmCyan, Green Fluorescent Protein (GFP). An additional preferred screenable marker gene is lac.

The invention also contemplates novel methods of screening for adchromosomal plant cells that involve use of relatively low, sub-killing concentrations of selection agent (e.g. sub-killing antibiotic concentrations), and also involve use of a screenable marker (e.g., a visible marker gene) to identify clusters of modified cells carrying the screenable marker, after which these screenable cells are manipulated to homogeneity. As used herein, a “selectable marker” is a gene whose presence results in a clear phenotype, and most often a growth advantage for cells that contain the marker. This growth advantage may be present under standard conditions, altered conditions such as elevated temperature, specialized media compositions, or in the presence of certain chemicals such as herbicides or antibiotics. Use of selectable markers is described, for example, in Broach et al. Gene, 8:121-133, 1979. Examples of selectable markers include the thymidine kinase gene, the cellular adenine phosphoribosyltransferase gene and the dihydrylfolate reductase gene, hygromycin phosphotransferase genes, the bar gene, neomycin phosphotransferase genes and phosphomannose isomerase, among others. Preferred selectable markers in the present invention include genes whose expression confer antibiotic or herbicide resistance to the host cell, or proteins allowing utilization of a carbon source not normally utilized by plant cells. Expression of one of these markers should be sufficient to enable the maintenance of a vector within the host cell, and facilitate the manipulation of the plasmid into new host cells. Of particular interest in the present invention are proteins conferring cellular resistance to kanamycin, G 418, paramomycin, hygromycin, bialaphos, and glyphosate for example, or proteins allowing utilization of a carbon source, such as mannose, not normally utilized by plant cells.

The term “stable” as used herein means that the mini-chromosome can be transmitted to daughter cells over at least 8 mitotic generations. Some embodiments of mini-chromosomes may be transmitted as functional, autonomous units for less than 8 mitotic generations, e.g. 1, 2, 3, 4, 5, 6, or 7. Preferred mini-chromosomes can be transmitted over at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 generations, for example, through the regeneration or differentiation of an entire plant, and preferably are transmitted through meiotic division to gametes. Other preferred mini-chromosomes can be further maintained in the zygote derived from such a gamete or in an embryo or endosperm derived from one or more such gametes. A “functional and stable” mini-chromosome is one in which functional mini-chromosomes can be detected after transmission of the mini-chromosomes over at least 8 mitotic generations, or after inheritance through a meiotic division. During mitotic division, as occurs occasionally with native chromosomes, there may be some non-transmission of mini-chromosomes; the mini-chromosome may still be characterized as stable despite the occurrence of such events if an adchromosomal plant that contains descendants of the mini-chromosome distributed throughout its parts may be regenerated from cells, cuttings, propagules, or cell cultures containing the mini-chromosome, or if an adchromosomal plant can be identified in progeny of the plant containing the mini-chromosome.

As used herein, a “structural gene” is a sequence which codes for a polypeptide or RNA and includes 5′ and 3′ ends. The structural gene may be from the host into which the structural gene is transformed or from another species. A structural gene will preferably, but not necessarily, include one or more regulatory sequences which modulate the expression of the structural gene, such as a promoter, terminator or enhancer. A structural gene will preferably, but not necessarily, confer some useful phenotype upon an organism comprising the structural gene, for example, herbicide resistance. In one embodiment of the invention, a structural gene may encode an RNA sequence which is not translated into a protein, for example a tRNA or rRNA gene.

As used herein, the term “telomere” or “telomere DNA” refers to a sequence capable of capping the ends of a chromosome, thereby preventing degradation of the chromosome end, ensuring replication and preventing fusion to other chromosome sequences. Telomeres can include naturally occurring telomere sequences or synthetic sequences. Telomeres from one species may confer telomere activity in another species. An exemplary telomere DNA is a heptanucleotide telomere repeat TTTAGGG (and its complement) found in the majority of plants.

“Transformed,” “transgenic,” “modified,” and “recombinant” refer to a host organism such as a plant into which an exogenous or heterologous nucleic acid molecule has been introduced, and includes meiocytes, seeds, zygotes, embryos, endosperm, or progeny of such plant that retain the exogenous or heterologous nucleic acid molecule but which have not themselves been subjected to the transformation process.

When the phrase “transmission efficiency” of a certain percent is used, transmission percent efficiency is calculated by measuring mini-chromosome presence through one or more mitotic or meiotic generations. It is directly measured as the ratio (expressed as a percentage) of the daughter cells or plants demonstrating presence of the mini-chromosome to parental cells or plants demonstrating presence of the mini-chromosome. Presence of the mini-chromosome in parental and daughter cells is demonstrated with assays that detect the presence of an exogenous nucleic acid carried on the mini-chromosome. Exemplary assays can be the detection of a screenable marker (e.g. presence of a fluorescent protein or any gene whose expression results in an observable phenotype), a selectable marker, or PCR amplification of any exogenous nucleic acid carried on the mini-chromosome.

Constructing Mini-Chromosomes by Site-Specific Recombination

Plant mini-chromosomes may be constructed using site-specific recombination sequences (for example those recognized by the bacteriophage P1 Cre recombinase, or the bacteriophage lambda integrase, or similar recombination enzymes). A compatible recombination site, or a pair of such sites, is present on both the centromere containing DNA clones and the donor DNA clones. Incubation of the donor clone and the centromere clone in the presence of the recombinase enzyme causes strand exchange to occur between the recombination sites in the two plasmids; the resulting mini-chromosomes contain centromere sequences as well as mini-chromosome vector sequences. The DNA molecules formed in such recombination reactions is introduced into E. coli, other bacteria, yeast or plant cells by common methods in the field including, but not limited to, heat shock, chemical transformation, electroporation, particle bombardment, whiskers, or other transformation method followed by selection for marker genes including chemical, enzymatic, color, or other marker present on either parental plasmid, allowing for the selection of transformants harboring mini-chromosomes.

II. Methods of Detecting and Characterizing Mini-Chromosomes in Plant Cells or of Scoring Mini-Chromosome Performance in Plant Cells:

Identification of Candidate Centromere Fragments by Probing BAC Libraries

Centromere clones are identified from a large genomic insert library such as a Bacterial Artificial Chromosome library. Probes are labeled using nick-translation in the presence of radioactively labeled dCTP, dATP, dGTP or dTTP as in, for example, the commercially available Rediprime kit (Amersham) as per the manufacturer's instructions. Other labeling methods familiar to those skilled in the art could be substituted. The libraries are screened and deconvoluted. Genomic clones are screened by probing with small centromere-specific clones (for example 14F1 was used) which shows high homology to the satellite sequence (14F1 showed homology to “BJCANRD”, Genbank ID X68786.1). Other embodiments of this procedure would involve hybridizing a library with other centromere sequences. Of the BAC clones identified using this procedure, a representative set are identified as having high hybridization signals to some probes, and optionally low hybridization signals to other probes. These are selected, the bacterial clones grown up in cultures and DNA prepared by methods familiar to those skilled in the art such as alkaline lysis. The DNA composition of purified clones are surveyed using for example fingerprinting by digesting with restriction enzymes such as, but not limited to, HinfI or HindIII. In a preferred embodiment the restriction enzyme cuts within the tandem centromere satellite repeat (see below). A variety of clones showing different fingerprints are selected for conversion into mini-chromosomes and inheritance testing. It can also be informative to use multiple restriction enzymes for fingerprinting or other enzymes which can cleave DNA.

Fingerprinting Analysis of BACs and Mini-Chromosomes

Centromere function may be associated with large tandem arrays of satellite repeats. To assess the composition and architecture of the centromere BACs, the candidate BACs are digested with a restriction enzyme, such as HindIII, which cuts with known frequency within the consensus sequence of the unit repeat of the tandemly repeated centromere satellite. Digestion products are then separated by agarose gel electrophoresis. Large insert clones containing a large array of tandem repeats will produce a strong band of the unit repeat size, as well as less intense bands at 2× and 3× the unit repeat size, and further multiples of the repeat size. These methods are well-known and there are many possible variations known to those skilled in the art.

Determining Sequence Composition of Mini-Chromosomes by Shotgun Cloning/Sequencing, Sequence Analysis

To determine the sequence composition of the mini-chromosome, the insert is sequenced. To generate DNA suitable for sequencing mini-chromosomes are fragmented, for example by using a random shearing method (such as sonication, nebulization, etc). Other fragmentation techniques may also be used such as enzymatic digestion. These fragments are then cloned into a plasmid vector and sequenced. The resulting DNA sequence is trimmed of poor-quality sequence and of sequence corresponding to the plasmid vector. The sequence is then compared to the known DNA sequences using an algorithm such as BLAST to search a sequence database such as GenBank.

To determine the consensus of the satellite repeat in the mini-chromosome, the sequences containing satellite repeat are aligned using a DNA sequence alignment program such as ContigExpress from Vector NTI. The sequences may also be aligned to previously determined repeats for that species. The sequences are trimmed to unit repeat length using the consensus as a template. Sequences trimmed from the ends of the alignment are realigned with the consensus and further trimmed until all sequences are at or below the consensus length. The sequences are then aligned with each other. The consensus is determined by the frequency of a specific nucleotide at each position; if the most frequent base is three times more frequent than the next most frequent base, it was considered the consensus.

Methods for determining consensus sequence are well known in the art, see, e.g., U.S. Pat. App. Pub. No. 20030124561; Hall & Preuss (2002). These methods, including DNA sequencing, assembly, and analysis, are well-known and there are many possible variations known to those skilled in the art. Other alignment parameters may also be useful such as using more or less stringent definitions of consensus.

Non-Selective Mini-Chromosome Mitotic Inheritance Assays

The following list of assays and potential outcomes illustrates how various assays can be used to distinguish autonomous events from integrated events.

Assay #1: Transient Assay

Mini-chromosomes are tested for their ability to become established as chromosomes and their ability to be inherited in mitotic cell divisions. In this assay, mini-chromosomes are delivered to plant cells, for example Brassica suspension cells in liquid culture. The cells used can be at various stages of growth. In this example, a population in which some cells were undergoing division was used. The mini-chromosome is then assessed over the course of several cell divisions, by tracking the presence of a screenable marker, e.g. a visible marker gene such as a fluorescent protein. Mini-chromosomes that are inherited well may show an initial delivery into many single cells; after several cell divisions, these single cells divide to form clusters of mini-chromosome-containing cells. Other exemplary embodiments of this method include delivering mini-chromosomes to other mitotic cell types, including roots and shoot meristems.

Assay #2: Non-Lineage Based Inheritance Assays on Modified Transformed Cells and Plants

Mini-chromosome inheritance is assessed on modified cell lines and plants by following the presence of the mini-chromosome over the course of multiple cell divisions. An initial population of mini-chromosome containing cells is assayed for the presence of the mini-chromosome, by the presence of a marker gene, including but not limited to a fluorescent protein, a colored protein, a protein assayable by histochemical assay, and a gene affecting cell morphology. All nuclei are stained with a DNA-specific dye including but not limited to DAPI, Hoechst 33258, OliGreen, Giemsa YOYO, or TOTO, allowing a determination of the number of cells that do not contain the mini-chromosome. After the initial determination of the percent of cells carrying the mini-chromosome, the cells are allowed to divide over the course of several cell divisions. The number of cell divisions, n, is determined by a method including but not limited to monitoring the change in total weight of cells, and monitoring the change in volume of the cells or by directly counting cells in an aliquot of the culture. After a number of cell divisions, the population of cells is again assayed for the presence of the mini-chromosome. The loss rate per generation is calculated by the equation: Loss rate per generation=1−(F/1)^(l/n)

The population of mini-chromosome-containing cells may include suspension cells, roots, leaves, meristems, flowers, or any other tissue of modified plants, or any other cell type containing a mini-chromosome.

These methods are well-known and there are many possible variations known to those skilled in the art; they have been used before with human cells and yeast cells.

Assay #3: Lineage Based Inheritance Assays on Modified Cells and Plants

Mini-chromosome inheritance is assessed on modified cell lines and plants by following the presence of the mini-chromosome over the course of multiple cell divisions. In cell types that allow for tracking of cell lineage, including but not limited to root cell files, trichomes, and leaf stomata guard cells, mini-chromosome loss per generation does not need to be determined statistically over a population, it can be discerned directly through successive cell divisions. In other manifestations of this method, cell lineage can be discerned from cell position, or methods including but not limited to the use of histological lineage tracing dyes, and the induction of genetic mosaics in dividing cells.

In one simple example, the two guard cells of the stomata are daughters of a single precursor cell. To assay mini-chromosome inheritance in this cell type, the epidermis of the leaf of a plant containing a mini-chromosome is examined for the presence of the mini-chromosome by the presence of a marker gene, including but not limited to a fluorescent protein, a colored protein, a protein assayable by histochemical assay, and a gene affecting cell morphology. The number of loss events in which one guard cell contains the mini-chromosome (L) and the number of cell divisions in which both guard cells contain the mini-chromosome (B) are counted. The loss rate per cell division is determined as L/(L+B). Other lineage-based cell types are assayed in similar fashion. These methods are well-known and there are many possible variations known to those skilled in the art; they have been used before with yeast cells.

Lineal mini-chromosome inheritance may also be assessed by examining root files (e.g. Brassica root files) or clustered cells in callus (e.g. soybean callus) over time. Changes in the percent of cells carrying the mini-chromosome will indicate the mitotic inheritance.

Assay #4: Inheritance Assays on Modified Cells and Plants in the Presence of Chromosome Loss Agents

Any of the above three assays can be done in the presence of chromosome loss agents. (including but not limited to colchicine, colcemid, caffeine, etopocide, nocodazole, oryzalin, trifluran). It is likely that an autonomous mini-chromosome will prove more susceptible to loss induced by chromosome loss agents; therefore, autonomous mini-chromosomes should show a lower rate of inheritance in the presence of chromosome loss agents. These methods have been used to study chromosome loss in fruit flies and yeast; there are many possible variations known to those skilled in the art.

III. Transformation of Plant Cells and Plant Regeneration

Various methods may be used to deliver DNA into plant cells. These include biological methods, such as Agrobacterium, E. coli, and viruses, physical methods such as biolistic particle bombardment, nanocopoiea device, the Stein beam gun silicon, carbide whiskers and microinjection, electrical methods such as electroporation, and chemical methods such as the use of poly-ethylene glycol and other compounds known to stimulate DNA uptake into cells. Examples of these techniques are described by Paszkowski et al., EMBO J. 3: 2717-2722 (1984), Potrykus et al., Mol. Gen. Genet. 199: 169-177 (1985), Reich et al., Biotechnology 4: 1001-1004 (1986), and Klein et al., Nature 327: 70-73 (1987). Transformation using silicon carbide whiskers, e.g. in maize, is described in Brisibe, J. Exp. Bot. 51(343):187-196 (2000) and Dunwell, Methods Mol. Biol. 111:375-82 (1999) and U.S. Pat. No. 5,464,765.

Agrobacterium-Mediated Delivery

Agrobacterium-mediated transformation is one method for introducing a desired genetic element into a plant. Several Agrobacterium species mediate the transfer of a specific DNA known as “T-DNA” that can be genetically engineered to carry a desired piece of DNA into many plant species. Plasmids used for delivery contain the T-DNA flanking the nucleic acid to be inserted into the plant. The major events marking the process of T-DNA mediated pathogenesis are induction of virulence genes, processing and transfer of T-DNA.

There are three common methods to transform plant cells with Agrobacterium. The first method is co-cultivation of Agrobacterium with cultured isolated protoplasts. This method requires an established culture system that allows culturing protoplasts and plant regeneration from cultured protoplasts. The second method is transformation of cells or tissues with Agrobacterium. This method requires (a) that the plant cells or tissues can be modified by Agrobacterium and (b) that the modified cells or tissues can be induced to regenerate into whole plants. The third method is transformation of seeds, apices or meristems with Agrobacterium. This method requires exposure of the meristematic cells of these tissues to Agrobacterium and micropropagation of the shoots or plan organs arising from these meristematic cells.

Those of skill in the art are familiar with procedures for growth and suitable culture conditions for Agrobacterium as well as subsequent inoculation procedures. Liquid or semi-solid culture media can be used. The density of the Agrobacterium culture used for inoculation and the ratio of Agrobacterium cells to explant can vary from one system to the next, as can media, growth procedures, timing and lighting conditions.

Transformation of dicotyledons using Agrobacterium has long been known in the art, and transformation of monocotyledons using Agrobacterium has also been described. See, WO 94/00977 and U.S. Pat. No. 5,591,616, both of which are incorporated herein by reference. See also, Negrotto et al., Plant Cell Reports 19: 798-803 (2000), incorporated herein by reference.

A number of wild-type and disarmed strains of Agrobacterium tumefaciens and Agrobacterium rhizogenes harboring Ti or Ri plasmids can be used for gene transfer into plants. Preferably, the Agrobacterium hosts contain disarmed Ti and Ri plasmids that do not contain the oncogenes that cause tumorigenesis or rhizogenesis. Exemplary strains include Agrobacterium tumefaciens strain C58, a nopaline-type strain that is used to mediate the transfer of DNA into a plant cell, octopine-type strains such as LBA4404 or succinamopine-type strains, e.g., EHA101 or EHA105. The use of these strains for plant transformation has been reported and the methods are familiar to those of skill in the art.

U.S. Application No. 20040244075 published Dec. 2, 2004 describes improved methods of Agrobacterium-mediated transformation. The efficiency of transformation by Agrobacterium may be enhanced by using a number of methods known in the art. For example, the inclusion of a natural wound response molecule such as acetosyringone (AS) to the Agrobacterium culture has been shown to enhance transformation efficiency with Agrobacterium tumefaciens (Shahla et al., (1987) Plant Molec. Biol. 8:291-298). Alternatively, transformation efficiency may be enhanced by wounding the target tissue to be modified or transformed. Wounding of plant tissue may be achieved, for example, by punching, maceration, bombardment with microprojectiles, etc. (See e.g., Bidney et al., (1992) Plant Molec. Biol. 18:301-313).

In addition, a recent method described by Broothaerts, et. al. (Nature 433: 629-633, 2005) expands the bacterial genera that can be used to transfer genes into plants. This work involved the transfer of a disarmed Ti plasmid without T-DNA and another vector with T-DNA containing the marker enzyme beta-glucuronidase, into three different bacteria. Gene transfer was successful and this method significantly expands the tools available for gene delivery into plants.

Microprojectile Bombardment Delivery

Another widely used technique to genetically transform plants involves the use of microprojectile bombardment. In this process, a nucleic acid containing the desired genetic elements to be introduced into the plant is deposited on or in small dense particles, e.g., tungsten, platinum, or preferably 1 micron gold particles, which are then delivered at a high velocity into the plant tissue or plant cells using a specialized biolistics device. Many such devices have been designed and constructed; one in particular, the PDS1000/He sold by BioRad, is the instrument most commonly used for biolistics of plant cells. The advantage of this method is that no specialized sequences need to be present on the nucleic acid molecule to be delivered into plant cells; delivery of any nucleic acid sequence is theoretically possible.

For the bombardment, cells in suspension are concentrated on filters or solid culture medium. Alternatively, immature embryos, seedling explants, or any plant tissue or target cells may be arranged on solid culture medium. The cells to be bombarded are positioned at an appropriate distance below the microprojectile stopping plate.

Various biolistics protocols have been described that differ in the type of particle or the manner in which DNA is coated onto the particle. Any technique for coating microprojectiles that allows for delivery of transforming DNA to the target cells may be used. For example, particles may be prepared by functionalizing the surface of a gold oxide particle, providing free amine groups. DNA, having a strong negative charge, binds to the functionalized particles.

Parameters such as the concentration of DNA used to coat microprojectiles may influence the recovery of transformants containing a single copy of the transgene. For example, a lower concentration of DNA may not necessarily change the efficiency of the transformation but may instead increase the proportion of single copy insertion events. In this regard, ranges of approximately 1 ng to approximately 10 μg (10,000 ng), approximately 5 ng to 8 μg or approximately 20 ng, 50 ng, 100 ng, 200 ng, 500 ng, 1 μg, 2 μg, 5 μg, or 7 μg of transforming DNA may be used per each 1.0-2.0 mg of starting 1.0 micron gold particles.

Other physical and biological parameters may be varied, such as manipulation of the DNA/microprojectile precipitate, factors that affect the flight and velocity of the projectiles, manipulation of the cells before and immediately after bombardment (including osmotic state, tissue hydration and the subculture stage or cell cycle of the recipient cells), the orientation of an immature embryo or other target tissue relative to the particle trajectory, and also the nature of the transforming DNA, such as linearized DNA or intact supercoiled plasmids. One may particularly wish to adjust physical parameters such as DNA concentration, gap distance, flight distance, tissue distance, and helium pressure.

The particles delivered via biolistics can be “dry” or “wet.” In the “dry” method, the mini-chromosome DNA-coated particles such as gold are applied onto a macrocarrier (such as a metal plate, or a carrier sheet made of a fragile material such as mylar) and dried. The gas discharge then accelerates the macrocarrier into a stopping screen, which halts the macrocarrier but allows the particles to pass through; the particles then continue their trajectory until they impact the tissue being bombarded. For the “wet” method, the droplet containing the mini-chromosome DNA-coated particles is applied to the bottom part of a filter holder, which is attached to a base which is itself attached to a rupture disk holder used to hold the rupture disk to the helium egress tube for bombardment. The gas discharge directly displaces the DNA/gold droplet from the filter holder and accelerates the particles and their DNA cargo into the tissue being bombarded. The wet biolistics method has been described in detail elsewhere but has not previously been applied in the context of plants (Mialhe et al., Mol Mar Biol Biotechnol. 4(4):275-831995). The concentrations of the various components for coating particles and the physical parameters for delivery can be optimized using procedures known in the art.

A variety of plant cells/tissues are suitable for transformation, including immature embryos, scutellar tissue, suspension cell cultures, immature inflorescence, shoot meristem, epithelial peels, nodal explants, callus tissue, hypocotyl tissue, cotyledons, roots, and leaves, meristem cells, and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant may be regenerated is useful as a recipient cell. Callus may be initiated from tissue sources including, but not limited to, immature embryos, seedling apical meristems, microspore-derived embryos, roots, hypocotyls, cotyledons and the like. Those cells which are capable of proliferating as callus also are recipient cells for genetic transformation.

Any suitable plant culture medium can be used. Examples of suitable media would include but are not limited to MS-based media (Murashige and Skoog, Physiol. Plant, 15:473-497, 1962) or N6-based media(Chu et al., Scientia Sinica 18:659, 1975) supplemented with additional plant growth regulators including but not limited to auxins such as picloram (4-amino-3,5,6-trichloropicolinic acid), 2,4-D (2,4-dichlorophenoxyacetic acid), naphalene-acetic acid (NAA) and dicamba (3,6-dichloroanisic acid), cytokinins such as BAP (6-benzylaminopurine) and kinetin, and gibberellins. Other media additives can include but are not limited to amino acids, macroelements, iron, microelements, vitamins and organics, carbohydrates, undefined media components such as casein hydrolysates, an appropriate gelling agent such as a form of agar, a low melting point agarose or Gelrite if desired. Those of skill in the art are familiar with the variety of tissue culture media, which when supplemented appropriately, support plant tissue growth and development and are suitable for plant transformation and regeneration. These tissue culture media can either be purchased as a commercial preparation, or custom prepared and modified. Examples of such media would include but are not limited to Murashige and Skoog (Mursahige and Skoog, Physiol. Plant, 15:473-497, 1962), N6 (Chu et al., Scientia Sinica 18:659, 1975), Linsmaier and Skoog (Linsmaier and Skoog, Physio. Plant., 18:100, 1965), Uchimiya and Murashige (Uchimiya and Murashige, Plant Physiol. 15:473, 1962), Gamborg's B5 media (Gamborg et al., Exp. Cell Res., 50:151, 1968), D medium (Duncan et al., Planta, 165:322-332, 1985), Mc-Cown's Woody plant media (McCown and Lloyd, HortScience 6:453, 1981), Nitsch and Nitsch (Nitsch and Nitsch, Science 163:85-87, 1969), and Schenk and Hildebrandt (Schenk and Hildebrandt, Can. J. Bot. 50:199-204, 1972) or derivations of these media supplemented accordingly. Those of skill in the art are aware that media and media supplements such as nutrients and growth regulators for use in transformation and regeneration and other culture conditions such as light intensity during incubation, pH, and incubation temperatures can be varied.

Those of skill in the art are aware of the numerous modifications in selective regimes, media, and growth conditions that can be varied depending on the plant system and the selective agent. Typical selective agents include but are not limited to antibiotics such as geneticin (G418), kanamycin, paromomycin or other chemicals such as glyphosate or other herbicides. Consequently, such media and culture conditions disclosed in the present invention can be modified or substituted with nutritionally equivalent components, or similar processes for selection and recovery of transgenic events, and still fall within the scope of the present invention.

Mini-Chromosome Delivery without Selection

Mini-chromosome is delivered to plant cells or tissues, e.g., plant cells in suspension to obtain stably modified callus clones for inheritance assay. Suspension cells are maintained in a growth media, for example Murashige and Skoog (MS) liquid medium containing an auxin such as 2,4-dichlorophenoxyacetic acid (2,4-D). Cells are bombarded using a particle bombardment process, such as the helium-driven PDS-1000/He system, and propagated in the same liquid medium to permit the growth of modified and non-modified cells. Portions of each bombardment are monitored for formation of fluorescent clusters, which are isolated by micromanipulation and cultured on solid medium. Clones modified with mini-chromosome are expanded and homogenous clones are used in inheritance assays, or assays measuring mini-chromosome structure or autonomy.

Mini-Chromosome Transformation with Selectable Marker Gene

Isolation of mini-chromosome-modified cells in bombarded calluses or explants can be facilitated by the use of a selectable marker gene. The bombarded tissues are transferred to a medium containing an appropriate selective agent for a particular selectable marker gene. Such a transfer usually occurs between 0 and about 7 days after bombardment. The transfer could also take place any number of days after bombardment. The amount of selective agent and timing of incorporation of such an agent in selection medium can be optimized by using procedures known in the art. Selection inhibits the growth of non-modified cells, thus providing an advantage to the growth of modified cells, which can be further monitored by tracking the presence of a fluorescent marker gene or by the appearance of modified explants (modified cells on explants may be green under light in selection medium, while surrounding non-modified cells are weakly pigmented). In plants that develop through shoot organogenesis (e.g. Brassica, tomato or tobacco), the modified cells can form shoots directly, or alternatively, can be isolated and expanded for regeneration of multiple shoots transgenic for mini-chromosome. In plants that develop through embryogenesis (e.g. corn or soybean), additional culturing steps may be necessary to induce the modified cells to form an embryo and to regenerate in the appropriate media.

Useful selectable marker genes are well known in the art and include, for example, herbicide and antibiotic resistance genes including but not limited to neomycin phosphotransferase II (conferring resistance to kanamycin, paramomycin and G418), hygromycin phosphotransferase (conferring resistance to hygromycin), 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS, conferring resistance to glyphosate), phosphinothricin acetyltransferase (conferring resistance to phosphinothricin/bialophos), MerA (conferring resistance to mercuric ions). Selectable marker genes may be transformed using standard methods in the art.

The first step in the production of plants containing novel genes involves delivery of DNA into a suitable plant tissue (described in the previous section) and selection of the tissue under conditions that allow preferential growth of any cells containing the novel genes. Selection is typically achieved with a selectable marker gene present in the delivered DNA, which may be a gene conferring resistance to an antibiotic, herbicide or other killing agent, or a gene allowing utilization of a carbon source not normally metabolized by plant cells. For selection to be effective, the plant cells or tissue need to be grown on selective medium containing the appropriate concentration of antibiotic or killing agent, and the cells need to be plated at a defined and constant density. The concentration of selective agent and cell density are generally chosen to cause complete growth inhibition of wild type plant tissue that does not express the selectable marker gene; but allowing cells containing the introduced DNA to grow and expand into adchromosomal clones. This critical concentration of selective agent typically is the lowest concentration at which there is complete growth inhibition of wild type cells, at the cell density used in the experiments. However, in some cases, sub-killing concentrations of the selective agent may be equally or more effective for the isolation of plant cells containing mini-chromosome DNA, especially in cases where the identification of such cells is assisted by a visible marker gene (e.g., fluorescent protein gene) present on the mini-chromosome.

In some species (e.g., tobacco or tomato), a homogenous clone of modified cells can also arise spontaneously when bombarded cells are placed under the appropriate selection. An exemplary selective agent is the neomycin phosphotransferase II (nptII) marker gene, which is commonly used in plant biotechnology and confers resistance to the antibiotics kanamycin, G418 (geneticin) and paramomycin. In other species, or in certain plant tissues or when using particular selectable markers, homogeneous clones may not arise spontaneously under selection; in this case the clusters of modified cells can be manipulated to homogeneity using the visible marker genes present on the mini-chromosomes as an indication of which cells contain mini-chromosome DNA.

Regeneration of Adchromosomal Plants from Explants to Mature, Rooted Plants

For plants that develop through shoot organogenesis (e.g. Brassica, tomato and tobacco), regeneration of a whole plant involves culturing of regenerable explant tissues taken from sterile organogenic callus tissue, seedlings or mature plants on a shoot regeneration medium for shoot organogenesis, and rooting of the regenerated shoots in a rooting medium to obtain intact whole plants with a fully developed root system. These plants are potted in soil and grown to maturity in a greenhouse.

For plant species, such corn and soybean, regeneration of a whole plant occurs via an embryogenic step that is not necessary for plant species where shoot organogenesis is efficient. In these plants the explant tissue is cultured on an appropriate media for embryogenesis, and the embryo is cultured until shoots form. The regenerated shoots are cultured in a rooting medium to obtain intact whole plants with a fully developed root system. These plants are potted in soil and grown to maturity in a greenhouse.

Explants are obtained from any tissues of a plant suitable for regeneration. Exemplary tissues include hypocotyls, internodes, roots, cotyledons, petioles, cotyledonary petioles, leaves and peduncles, prepared from sterile seedlings or mature plants. Brassica tissue can be from any Brassica species such as Brassica napus, Brassica oleraceae, Brassica nigra, Brassica carinata, Brassica juncea, and Brassica campestris.

Explants are wounded (for example with a scalpel or razor blade) and cultured on a shoot regeneration medium (SRM) containing Murashige and Skoog (MS) medium as well as a cytokinin, e.g., 6-benzylaminopurine (BA), and an auxin, e.g., α-naphthaleneacetic acid (NAA), and an anti-ethylene agent, e.g., silver nitrate (AgNO₃). For example, 2 mg/L of BA, 0.05 mg/L of NAA, and 2 mg/L of AgNO₃ can be added to MS medium for shoot organogenesis. The most efficient shoot regeneration is obtained from longitudinal sections of internode explants.

Shoots regenerated via organogenesis are rooted in a MS medium containing low concentration of an auxin such as NAA. Plants are potted and grown in a greenhouse to sexual maturity for seed harvest.

To regenerate a whole plant with a mini-chromosome, explants are pre-incubated for 1 to 7 days (or longer) on the shoot regeneration medium prior to bombardment with mini-chromosome (see below). Following bombardment, explants are incubated on the same shoot regeneration medium for a recovery period up to 7 days (or longer), followed by selection for transformed shoots or clusters on the same medium but with a selective agent appropriate for a particular selectable marker gene (see below).

Method of Co-Delivering Growth Inducing Genes to Facilitate Isolation of Adchromosomal Plant Cell Clones

Another method used in the generation of cell clones containing mini-chromosomes involves the co-delivery of DNA containing genes that are capable of activating growth of plant cells, or that promote the formation of a specific organ, embryo or plant structure that is capable of self-sustaining growth. In one embodiment, the recipient cell receives simultaneously the mini-chromosome, and a separate DNA molecule encoding one or more growth promoting, organogenesis-promoting, embryogenesis-promoting or regeneration-promoting genes. Following DNA delivery, expression of the plant growth regulator genes stimulates the plant cells to divide, or to initiate differentiation into a specific organ, embryo, or other cell types or tissues capable of regeneration. Multiple plant growth regulator genes can be combined on the same molecule, or co-bombarded on separate molecules. Use of these genes can also be combined with application of plant growth regulator molecules into the medium used to culture the plant cells, or of precursors to such molecules that are converted to functional plant growth regulators by the plant cell's biosynthetic machinery, or by the genes delivered into the plant cell.

The co-bombardment strategy of mini-chromosomes with separate DNA molecules encoding plant growth regulators transiently supplies the plant growth regulator genes for several generations of plant cells following DNA delivery. During this time, the mini-chromosome may be stabilized by virtue of its centromere, but the DNA molecules encoding plant growth regulator genes, or organogenesis-promoting, embryogenesis-promoting or regeneration-promoting genes will tend to be lost. The transient expression of these genes, prior to their loss, may give the cells containing mini-chromosome DNA a sufficient growth advantage, or sufficient tendency to develop into plant organs, embryos or a regenerable cell cluster, to outgrow the non-modified cells in their vicinity, or to form a readily identifiable structure that is not formed by non-modified cells. Loss of the DNA molecule encoding these genes will prevent phenotypes from manifesting themselves that may be caused by these genes if present through the remainder of plant regeneration. In rare cases, the DNA molecules encoding plant growth regulator genes will integrate into the host plant's genome or into the mini-chromosome.

As described in Example 3, mini-chromosome DNA has been be co-delivered into plant cells together with DNA encoding genes that promote plant cell growth. Under a different embodiment of this invention, the genes promoting plant cell growth may be genes promoting shoot formation or embryogenesis, or giving rise to any identifiable organ, tissue or structure that can be regenerated into a plant. In this case, it may be possible to obtain embryos or shoots harboring mini-chromosomes directly after DNA delivery, without the need to induce shoot formation with growth activators supplied into the medium, or lowering the growth activator treatment necessary to regenerate plants. The advantages of this method are more rapid regeneration, higher transformation efficiency, lower background growth of non-modified tissue, and lower rates of morphologic abnormalities in the regenerated plants (due to shorter and less intense treatments of the tissue with chemical plant growth activators added to the growth medium).

Determination of Mini-Chromosome Structure an Autonomy in Adchromosomal Plants and Tissues

The structure and autonomy of the mini-chromosome in adchromosomal plants and tissues can be determined by methods including but not limited to: conventional and pulsed-field Southern blot hybridization to genomic DNA from modified tissue subjected or not subjected to restriction endonuclease digestion, dot blot hybridization of genomic DNA from modified tissue hybridized with different mini-chromosome specific sequences, PCR on DNA from modified tissues with probes specific to the mini-chromosome, or Fluorescence In Situ Hybridization to nuclei of modified cells. The table below summarizes these methods.

Assay Assay details Potential outcome Interpretation Southern blot Restriction digest of Native sizes and pattern Autonomous or genomic DNA* of bands integrated via CEN compared to purified fragment mini-C Altered sizes or pattern Integrated or rearranged of bands CHEF gel Southern Restriction digest of Native sizes and pattern Autonomous or blot genomic DNA of bands integrated via CEN compared to purified fragment mini-C Altered sizes or pattern Integrated or rearranged of bands Native genomic DNA Mini-C band migrating Autonomous circles or (no digest) ahead of genomic DNA linears present in plant Mini-C band co- Integrated migrating with genomic DNA >1 mini-C bands Various possibilities observed Exonuclease assay Exonuclease digestion Signal strength close to Autonomous circles of genomic DNA that w/o exonuclease present followed by detection No signal or signal Integrated of circular mini- strength lower that w/o chromosome by PCR, exonuclease dot blot, or restriction digest (optional), electrophoresis and southern blot (useful for circular mini- chromosomes) Mini-chromosome Transformation of Colonies isolated only Autonomous circles rescue plant genomic DNA from mini-C plants with present, native mini-C into E. coli followed by mini-Cs, not from structure selection for antibiotic controls; mini-C resistance genes on structure matches that of mini-C the parental mini-C Colonies isolated only Autonomous circles from mini-C plants with present, rearranged mini-Cs, not from mini-C structure OR controls; mini-C mini-Cs integrated via structure different from centromere fragment parental mini-C Colonies observed both Various possibilities in mini-C-modified plants and in controls PCR PCR amplification of All mini-c parts Complete mini-C various parts of the detected by PCR sequences present in mini-chromosome plant Subset of mini-c parts Partial mini-C detected by PCR sequences present in plant FISH Detection of mini- Mini-C sequences autonomous chromosome sequences detected, free of genome in mitotic or meiotic Mini-C sequences integrated nuclei by fluorescence detected, associated in situ hybridization with genome Mini-C sequences Both autonomous and detected, both free and integrated mini-C associated with genome sequences present No mini-C sequences Mini-C DNA not visible detected by FISH *Genomic DNA refers to total DNA extracted from plants containing a mini-chromosome

Furthermore, mini-chromosome structure can be examined by characterizing mini-chromosomes ‘rescued’ from adchromosomal cells. Circular mini-chromosomes that contain bacterial sequences for their selection and propagation in bacteria can be rescued from an adchromosomal plant or plant cell and re-introduced into bacteria. If no loss of sequences has occurred during replication of the mini-chromosome in plant cells, the mini-chromosome is able to replicate in bacteria and confer antibiotic resistance. Total genomic DNA is isolated from the adchromosomal plant cells by any method for DNA isolation known to those skilled in the art, including but not limited to a standard cetyltrimethylammonium bromide (CTAB) based method (Current Protocols in Molecular Biology (1994) John Wiley & Sons, N.Y., 2.3) The purified genomic DNA is introduced into bacteria (e.g., E. coli) using methods familiar to one skilled in the art (for example heat shock or electroporation). The transformed bacteria are plated on solid medium containing antibiotics to select bacterial clones modified with mini-chromosome DNA. Modified bacterial clones are grown up, the plasmid DNA purified (by alkaline lysis for example), and DNA analyzed by restriction enzyme digestion and gel electrophoresis or by sequencing. Because plant-methylated DNA containing methylcytosine residues will be degraded by wild-type strains of E. coli, bacterial strains (e.g. DH10B) deficient in the genes encoding methylation restriction nucleases (e.g. the mcr and mrr gene loci in E. coli) are best suited for this type of analysis. Mini-chromosome rescue can be performed on any plant tissue or clone of plant cells modified with a mini-chromosome.

Circular mini-chromosomes that contain bacterial sequences for their selection and propagation in bacteria can be rescued from an adchromosomal plant or plant cell and re-introduced into bacteria. If no loss of sequences has occurred during replication of the mini-chromosome in plant cells, the mini-chromosome is able to replicate in bacteria and confer antibiotic resistance. Total genomic DNA is isolated from the adchromosomal plant cells by any method for DNA isolation known to those skilled in the art, including but not limited to a standard cetyltrimethylammonium bromide (CTAB) based method (Current Protocols in Molecular Biology (1994) John Wiley & Sons, N.Y., 2.3) The purified genomic DNA is introduced into bacteria (e.g. E. coli) using methods familiar to one skilled in the art (for example heat shock or electroporation). The transformed bacteria are plated on solid medium containing antibiotics to select bacterial clones modified with mini-chromosome DNA. Modified bacterial clones are grown up, the plasmid DNA purified (by alkaline lysis for example), and DNA analyzed by restriction enzyme digestion and gel electrophoresis or by sequencing. Because plant-methylated DNA containing methylcytosine residues will be degraded by wild-type strains of E. coli, bacterial strains (e.g. DH10B) deficient in the genes encoding methylation restriction nucleases (e.g. the mcr and mrr gene loci in E. coli) are best suited for this type of analysis. Mini-chromosome rescue can be performed on any plant tissue or clone of plant cells modified with a mini-chromosome.

Mini-Chromosome Autonomy Demonstration by In Situ Hybridization (ISH)

To assess whether the mini-chromosome is autonomous from the native plant chromosomes, or has integrated into the plant genome, In Situ Hybridization is carried out (Fluorescent In Situ Hybridization or FISH is particularly well suited to this purpose). In this assay, mitotic or meiotic tissue, such as root tips or meiocytes from the anther, possibly treated with metaphase arrest agents such as colchicines is obtained, and standard FISH methods are used to label both the centromere and sequences specific to the mini-chromosome. For example, for Brassica, the Brassica centromere is labeled using probes from sequence 14F1, which labels all Brassica chromosomes with one fluorescent tag (Molecular Probes Alexafluor 568, for example), and sequences specific to the mini-chromosome are labeled with another fluorescent tag (Alexafluor 488, for example). All centromere sequences are detected with the first tag; only mini-chromosomes are detected with both the first and second tag. Chromosomes are stained with a DNA-specific dye including but not limited to DAN., Hoechst 33258, OliGreen, Giemsa YOYO, and TOTO. An autonomous mini-chromosome is visualized as a body that shows hybridization signal with both centromere probes and mini-chromosome specific probes and is separate from the native chromosomes. Similar procedures can be carried out for centromeres derived from other plant species.

Determination of Gene Expression Levels

The expression level of any gene present on the mini-chromosome can be determined by methods including but not limited to one of the following. The mRNA level of the gene can be determined by Northern Blot hybridization, Reverse Transcriptase-Polymerase Chain Reaction, binding levels of a specific RNA-binding protein, in situ hybridization, or dot blot hybridization.

The protein level of the gene product can be determined by Western blot hybridization, Enzyme-Linked Immunosorbant Assay (ELISA), fluorescent quantitation of a fluorescent gene product, enzymatic quantitation of an enzymatic gene product, immunohistochemical quantitation, or spectroscopic quantitation of a gene product that absorbs a specific wavelength of light.

Use of Exonuclease to Isolate Circular Mini-Chromosome DNA from Genomic DNA:

Exonucleases may be used to obtain pure mini-chromosome DNA, suitable for isolation of mini-chromosomes from E. coli or from plant cells. The method assumes a circular structure of the mini-chromosome. A DNA preparation containing mini-chromosome DNA and genomic DNA from the source organism is treated with exonuclease, for example lambda exonuclease combined with E. coli exonuclease I, or the ATP-dependent exonuclease (Qiagen Inc). Because the exonuclease is only active on DNA ends, it will specifically degrade the linear genomic DNA fragments, but will not affect the circular mini-chromosome DNA. The result is mini-chromosome DNA in pure form. The resultant mini-chromosome DNA can be detected by a number of methods for DNA detection known to those skilled in the art, including but not limited to PCR, dot blot followed by hybridization analysis, and southern blot followed by hybridization analysis. Exonuclease treatment followed by detection of resultant circular mini-chromosome may be used as a method to determine mini-chromosome autonomy.

Structural Analysis of Mini-Chromosomes by BAC-End Sequencing:

BAC-end sequencing procedures, known to those skilled in the art, can be applied to characterize mini-chromosome clones for a variety of purposes, such as structural characterization, determination of sequence content, and determination of the precise sequence at a unique site on the chromosome (for example the specific sequence signature found at the junction between a centromere fragment and the vector sequences). In particular, this method is useful to prove the relationship between a parental mini-chromosome and the mini-chromosomes descended from it and isolated from plant cells by mini-chromosome rescue, described above.

Methods for Scoring Meiotic Mini-Chromosome Inheritance

A variety of methods can be used to assess the efficiency of meiotic mini-chromosome transmission. In one embodiment of the method, gene expression of genes encoded by the mini-chromosome (marker genes or non-marker genes) can be scored by any method for detection of gene expression know to those skilled in the art, including but not limited to visible methods (e.g. fluorescence of fluorescent protein markers, scoring of visible phenotypes of the plant), scoring resistance of the plant or plant tissues to antibiotics, herbicides or other selective agents, by measuring enzyme activity of proteins encoded by the mini-chromosome, or measuring non-visible plant phenotypes, or directly measuring the RNA and protein products of gene expression using microarray, northern blots, in situ hybridization, dot blot hybridization, RT-PCR, western blots, immunoprecipitation, Enzyme-Linked Immunosorbant Assay (ELISA), immunofluorescence and radio-immunoassays (RIA). Gene expression can be scored in the post-meiotic stages of microspore, pollen, pollen tube or female gametophyte, or the post-zygotic stages such as embryo, seed, or progeny seedlings and plants. In another embodiment of the method, the mini-chromosome can de directly detected or visualized in post-meiotic, zygotic, embryonal or other cells in by a number of methods for DNA detection known to those skilled in the art, including but not limited to fluorescence in situ hybridization, in situ PCR, PCR, southern blot, or by mini-chromosome rescue described above.

FISH Analysis of Mini-Chromosome Copy Number in Meiocytes, Roots or Other Tissues of Adchromosomal Plants

The copy number of the mini-chromosome can be assessed in any cell or plant tissue by In Situ Hybridization (Fluorescent In Situ Hybridization or FISH is Particularly well suited to this purpose). In an exemplary assay, standard FISH methods are used to label the centromere (e.g., for Brassica, using probes from sequence 14F1 which labels all Brassica chromosomes with one fluorescent tag (Molecular Probes Alexafluor 568, for example)), and to label sequences specific to the mini-chromosome with another fluorescent tag (Alexafluor 488, for example). All centromere sequences are detected with the first tag; only mini-chromosomes are detected with both the first and second tag. Nuclei are stained with a DNA-specific dye including but not limited to DAPI, Hoechst 33258, OliGreen, Giemsa YOYO, and TOTO. Mini-chromosome copy number is determined by counting the number of fluorescent foci that label with both tags.

Induction of Callus and Roots from Adchromosomal Plants Tissues for Inheritance Assays

Mini-chromosome inheritance is assessed using callus and roots induced from transformed plants. To induce roots and callus, tissues such as leaf pieces are prepared from adchromosomal plants and cultured on a Murashige and Skoog (MS) medium containing a cytokinin, e.g., 6-benzylaminopurine (BA), and an auxin, e.g., α-naphthaleneacetic acid (NAA). Any tissue of an adchromosomal plant can be used for callus and root induction, and the medium recipe for tissue culture can be optimized using procedures known in the art.

Clonal Propagation of Adchromosomal Plants

To produce multiple clones of plants from a mini-chromosome-transformed plant, any tissue of the plant can be tissue-cultured for shoot organogenesis using regeneration procedures described under the section regeneration of plants from explants to mature, rooted plants (see above). Alternatively, multiple auxiliary buds can induced from a mini-chromosome-modified plant by excising the shoot tip, which can be rooted for a whole plant; each auxiliary bud can be rooted for a whole plant.

Scoring of Antibiotic- or Herbicide Resistance in Seedlings and Plants (Progeny of Self- and Out-Crossed Transformants

Progeny seeds harvested from mini-chromosome-modified plants can be scored for antibiotic- or herbicide resistance by seed germination under sterile conditions on a growth media (for example Murashige and Skoog (MS) medium) containing an appropriate selective agent for a particular selectable marker gene. Only seeds containing the mini-chromosome can germinate on the medium and further grow and develop into whole plants. Alternatively, seeds can be germinated in soil, and the germinating seedlings can then be sprayed with a selective agent appropriate for a selectable marker gene. Seedlings that do not contain mini-chromosome do not survive; only seedlings containing mini-chromosome can survive and develop into mature plants.

Genetic Methods for Analyzing Mini-Chromosome Performance:

In addition to direct transformation of a plant with a mini-chromosome, plants containing a mini-chromosome can be prepared by crossing a first plant containing the functional, stable, autonomous mini-chromosome with a second plant lacking the construct.

Fertile plants modified with mini-chromosomes can be crossed to other plant lines or plant varieties to study mini-chromosome performance and inheritance. In the first embodiment of this method, pollen from an adchromosomal plant can be used to fertilize the stigma of a non-adchromosomal plant. Mini-chromosome presence is scored in the progeny of this cross using the methods outlines in the preceding section. In the second embodiment, the reciprocal cross is performed by using pollen from a non-adchromosomal plant to fertilize the flowers of a adchromosomal plant. The rate of mini-chromosome inheritance in both crosses can be used to establish the frequencies of meiotic inheritance in male and female meiosis. In the third embodiment of this method, the progeny of one of the crosses just described are back-crossed to the non-adchromosomal parental line, and the progeny of this second cross are scored for the presence of genetic markers in the plant's natural chromosomes as well as the mini-chromosome. Scoring of a sufficient marker set against a sufficiently large set of progeny allows the determination of linkage or co-segregation of the mini-chromosome to specific chromosomes or chromosomal loci in the plant's genome. Genetic crosses performed for testing genetic linkage can be done with a variety of combinations of parental lines; such variations of the methods described are known to those skilled in the art.

It should be understood that various changes and modifications to the presently preferred embodiments described herein will be apparent to those skilled in the art. Such changes and modifications can be made without departing from the spirit and scope of the present invention and without diminishing its intended advantages. It is therefore intended that such changes and modifications be covered by the appended claims.

Example 1 Brassica Centromere Construction

BAC Library Construction

A Bacterial Artificial Chromosome (BAC) library was constructed from Brassica genomic DNA isolated from B. oleraceae variety “Wisconsin fastplants” and digested with the restriction enzyme MboI. This enzyme was chosen because it is methylation insensitive and therefore can be used to enrich BAC libraries for centromere DNA sequences.

Probe Identification and Selection

Three groups of Brassica repetitive genomic DNA including specific centromere-localized sequences, were initially compiled as candidate probes for hybridization with the BAC libraries (Table 3). These probes represented various classes of Brassica repetitive sequences including satellite repeats (heterochromatic/centromere-specific), rDNA, and hypermethylated DNA fractions.

Four probes were picked to interrogate the BAC libraries. These probes represented different groups of commonly found repetitive sequences in the Brassica genome. The probes selected (Table 3) were CANREP (the Brassica centromere satellite), rRNA (18S), HpaII (bulk methylated DNA purified from genomic DNA by failure to digest with the methylation-sensitive enzyme HpaII) and Sau3A (bulk methylated DNA purified from genomic DNA by failure to digest with the methylation-sensitive enzyme Sau3A1). The probes were prepared from cloned fragments or from bulk methylated DNA prepared from Brassica genomic DNA. Sequences from the clones used to prepare each probe are shown in Table 3. Probes were prepared and labeled with standard molecular biology methods.

TABLE 3 Brassica repetitive genomic sequence and BAC library probes Group GenBank Group # Name Probe Name Description Clone used for hyb accession* Reference or comment 1 rDNA B6A10 18S rRNA 5012-5-6-A10 AF207007.1 (SEQ ID NO: 27) 2 Cen BF1 CANREP 5012-5-14-F01 X68786.1 CANREP is one of a large family of repeat (SEQ ID NO: 28) sequences hit by this sequence: gi|860800|emb|X68786.1|BJCANRD B. juncea Xle7-2EB gene gi|860798|emb|X68784.1|BJCANRB B. juncea Xle4-7B gene gi|17706|emb|X12736.1|BCREPC Brassica campestris DNA for satellite 3 Bulk Bhpaii Purified N/A N/A repetitive methylated DNA DNA fraction Bsau Purified N/A N/A methylated DNA fraction *Accession number of BLAST hit; actual sequence has not been deposited in Genbank Library Interrogation and Data Analysis

The BAC clones from the libraries were spotted onto filters and the filters were hybridized with each of the probes to identify specific BAC clones that contain DNA from the group of sequences represented by the probe(s).

A total of 18,432 BAC clones from the library were interrogated with each of the probes described above using the following hybridization conditions: 0.5×SSC 0.25% SDS at 65 degrees for 15 minutes, followed by a wash at 65 degrees for a half hour. The hybridization intensities of the BAC clones with each probe were scanned to quantitate hybridization intensity for each clone. The outputs (scores of 1 to 10 based on the hybridization intensities, with 10 being the strongest hybridization intensity) were imported into a relational database, for further analysis and classification. The database contained a total of four tables. Each table contained at total of 18,432 entries: the hybridization scores of each BAC clone from the library to one of the probes used to interrogate the library. Data analysis was done using standard SQL (Structured Query Language) routines to find BACs that contain different groups of repetitive sequences.

Classification and Selection of BAC Clones for Mini-chromosome Construction

BAC clones containing centromeric/heterochromatic DNA were identified by their hybridization scores to different probes. The goal was to select BAC clones that contained a diverse set of various repetitive sequences. Nine classes of centromeric BAC clones were eventually chosen to cover the broadest possible range of centromeric/heterochromatic sequences for mini-chromosome construction. Detailed descriptions of each class and probe hybridization values for each class are shown in Table 4.

TABLE 4 Classification of Brassica BAC clones containing centromeric DNA Class Probe Hybridization Range* # clones Class Properties CANREP HpaII Sau3A rDNA identified A Hi CANREP >=7 >=7 >=7 N/A 33 Hi Sau + Hpa B Hi CANREP >=7 N/A >=7 <=4 7 and Sau, Low rDNA C Hi Sau and N/A >=8 >=8 N/A 43 Hpa D Hi CANREP >=8 >=7 N/A N/A 123 and Hpa E Hi CANREP >=8 N/A >=7 N/A 59 and Sau F Hi CANREP >=7 <=4 <=4 N/A 15 only G Hi Sau only <=4 <=4 >=7 N/A 8 H Hi Hpa only <=4 >=7 <=4 N/A 58 I Hi >=7 4 to 6 4 to 6 N/A 210 CANREP, middle meth Total** 556 *Values represent hybridization intensities of an individual BAC to each probe on a scale of 1 to 10. Values were normalized. N/A = not applicable

A number of representative clones from each class were chosen to yield a total of 190 BAC clones for further analysis by restriction digest fingerprinting. The BAC clones were fingerprinted based on restriction sites found in the centromere specific sequence(s). Fingerprinting was used to evaluate the sequence composition of the large numbers of BAC clones and to compare their similarity to each other by comparing the restriction enzyme digest fragment patterns. A sequence with a tandem repeated sequence will show a single intense band of unit repeat size when digested with a restriction enzyme that cuts within the unit repeat. Second, BAC clones with similar sequences will show similar patterns of restriction fragments in a digest.

BAC DNA was extracted from bacteria using methods familiar to those skilled in the art. For Brassica, the restriction enzyme HindIII was used to digest the BAC clones. Colonies containing the BAC clones were grown overnight at 37° C. with shaking at 250-300 rpm. DNA from the colonies was isolated using Qiagen solution P1, Qiagen solution P2, Qiagen solution P3, followed by phenol/chloroform extraction. Subsequently, 10 μl of each DNA sample was inserted in into a well on a 96-well plate. The DNA samples were mixed with 10 μl of the following mixture: 200 μl 10× buffer (New England Biolabs), 50 ul 100×BSA (New England Biolabs), 30 μl enzyme (varies depending on Class of BAC clone) and 750 μl water. The samples were covered and incubated at 37° C. 1-4 hours. After the incubation, loading dye was added to each sample and the DNA was analyzed on a 1% agarose gel in 1×TBE, 23 volts for 14-18 hours.

For Brassica, the restriction enzyme HindIII was used to digest the BAC clones. After fingerprinting, 100 BACs were selected based on the fingerprint analysis in order to represent the hybridization classes, with an emphasis on the different classes containing the centromere tandem repeat. Within the hybridization classes, fingerprints showing the ‘simple ladder’ of ‘complex ladder’ patterns of bands at integer multiples of the unit centromere tandem repeat were favored. Additionally, within the hybridization classes, BAC clones that represent the diversity of fingerprints were preferred. Also, clones with matching fingerprints were not chosen. In some cases, after a round of functional testing, additional BACs were selected for their similarity of hybridization class and fingerprint to a BAC that showed good centromere function.

Twenty five BAC clones (from the original 190) were selected for mini-chromosome construction based on the fingerprint class. These BACs are listed in Table 5. Fingerprints were classified into 3 classes: 1. high complexity (multiple large bands with no indication of laddering), 2. low ladder (predominant bands at multiples of the unit repeat size for the centromere satellite, and 3. complex ladder (features of both previous types). Subsequent to testing, 4 additional BACs (BB221., BB222, BB229 and BB280) were chosen from the library based on their similarity to BB5 in both hybridization pattern and fingerprint. The preferred BACS have an *. Table 6 lists the fingerprint classes for 11 selected Brassica BACs.

TABLE 5 Restriction endonuclease fingerprinting of 25 Brassica BACs BAC BAC Hind III MiniC Number Class Class Properties Fingerprint Class tested BB2 A Hi CANREP, Meth 3. Complex ladder BB2R1-1 BB5* A Hi CANREP, Meth 3. Complex ladder BB5R4-1 BB5R4-3 BB7 B Hi CANREP, Meth, 1. Complex BB7R2-1 low rDNA BB11 D Hi CANREP, Meth 2. Simple ladder BB11R1-2 (Hpa) BB15 C Hi Meth 3. Complex ladder BB15R4-1 BB16* D Hi CANREP, Meth 1. Complex BB16R1-2 (Hpa) BB16R1-3 BB18* D Hi CANREP, Meth 1. Complex BB18R1-2 (Hpa) BB18R2-3 BB38* F Hi CANREP only 3. Complex ladder BB38R1-3 BB39 C Hi Meth n/d* BB39R1-3 BB40 C Hi Meth n/d* BB40R1-2 BB40R1-3 BB40R2-1 BB40R3-1 BB47* D Hi CANREP, Meth 2. Simple ladder BB47R1-2 (Hpa) BB52 E Hi CANREP, Meth 1. Complex BB52R1-1 (Sau) BB60* D Hi CANREP, Meth 3. Complex ladder BB60R1-1 (Hpa) BB63* D Hi CANREP, Meth 2. Simple ladder BB63R1-1 (Hpa) BB64 I Hi CANREP, 1. Complex BB64R1-1 Moderate Meth BB70* I Hi CANREP, 2. Simple ladder BB70R1-3 Moderate Meth BB71* E Hi CANREP, Meth 3. Complex ladder BB71R1-1 (Sau) BB76* I Hi CANREP, 1. Complex BB76R1-3 Moderate Meth BB102 D Hi CANREP, Meth n/d* BB102R1-1 (Hpa) BB104* I Hi CANREP, n/d* BB104R1-2 Moderate Meth BB105 I Hi CANREP, 2. Simple ladder BB105R1-2 Moderate Meth BB106 D Hi CANREP, Meth 2. Simple ladder BB106R1-2 (Hpa) BB119 I Hi CANREP, 3. Complex ladder BB119R1-1 Moderate Meth BB129 D Hi CANREP, Meth n/d* BB129R1-1 (Hpa) BB140 A Hi CANREP, Meth 2. Simple ladder BB140R1-3 BB221 A Hi CANREP, Meth 3. Complex ladder BB221R2-1 BB222 A Hi CANREP, Meth 3. Complex ladder BB222R2-7 BB229 A Hi CANREP, Meth 3. Complex ladder BB229R2-6 BB280 A Hi CANREP, Meth 3. Complex ladder BB280R2-3 n/d*: Gel too faint to score

TABLE 6 Restriction endonuclease fingerprint classification for 11 selected Brassica BACs BAC Hind III fingerprint Number Class Class Properties class BB5 A Hi CANREP, Meth 3. Complex ladder BB16 D Hi CANREP, Meth (Hpa) 1. Complex BB18 D Hi CANREP, Meth (Hpa) 1. Complex BB38 F Hi CANREP only 3. Complex ladder BB47 D Hi CANREP, Meth (Hpa) 2. Simple ladder BB60 D Hi CANREP, Meth (Hpa) 3. Complex ladder BB63 D Hi CANREP, Meth (Hpa) 2. Simple ladder BB70 I Hi CANREP, Moderate 2. Simple ladder Meth BB71 E Hi CANREP, Meth (Sau) 3. Complex ladder BB76 I Hi CANREP, Moderate 1. Complex Meth BB104 I Hi CANREP, Moderate n/d* Meth n/d*: Gel too faint to score

B. oleraceae (broccoli) BAC BB5 was deposited with the American Type Culture Collection (ATCC) P.O. Box 1549 Manassas, Va. 20108, USA on Feb. 23, 2005 and assigned Accession No. PT-6601.

To determine the molecular weight of centromere fragments in the BAC libraries, a frozen sample of bacteria harboring a BAC clone was grown in selective liquid media and the BAC DNA harvested using a standard alkaline lysis method. The recovered BAC DNA was restriction digested and resolved on an agarose gel. Centromere fragment size was determined by comparing to a molecular weight standard.

Cre/lox recombined donor DNA and BAC centromere DNA was delivered into bacteria and plated on selective solid media. To determine the molecular weight of centromere fragments in retrofitted mini-chromosomes, three bacterial colonies harboring a mini-chromosome were independently grown in selective liquid media and the BAC DNA harvested using a standard alkaline lysis method. The recovered BAC DNA was restriction digested and resolved on an agarose gel. Centromere fragment size was determined by comparing to a molecular weight standard. If variation in centromere size was noted, the mini-chromosome with the largest centromere insert was used for further experimentation.

Example 2 Assembly and Components of Brassica Mini-Chromosomes

Two methods have been developed to construct plant mini-chromosomes. The first method relies on cre/lox recombination in which a bacterial mini-chromosome (BAC) vector containing plant centromeric DNA and a loxP recombination site is recombined, by the action of cre recombinase, with a donor vector carrying plant gene expression cassettes to generate a plant mini-chromosome. The second method uses restriction enzyme digestion and ligation to produce two DNA fragments with compatible cohesive ends: 1) a vector fragment containing plant gene expression cassettes and ii) a centromere fragment. The two fragments are ligated into a circular structure to form a plant mini-chromosomes.

The components of the Brassica mini-chromosomes include fluorescent reporter genes, a selectable maker gene, a Brassica centromere sequence identified in a Brassica BAC library, a telomere sequence, a cloning vector and a donor vector. These components are described in detail below.

Mini-Chromosome Construction by Cre-Lox Recombination

Cre recombinase-mediated exchange was used to construct mini chromosomes by combining the plant centromere fragments cloned in pBeloBACT1 with a donor plasmid (e.g. pCHR151, Table 10). The recipient BAC vector carrying the plant centromere fragment contained a loxP recombination site; the donor plasmid contained two such sites, flanking the sequences to be inserted into the recipient BAC. Mini-chromosomes were constructed using a two-step method. First, the donor plasmid was linearized to allow free contact between the two loxP site; in this step the backbone of the donor plasmid is eliminated. In the second step, the donor molecules were combined with centromere BACs and were treated with Cre recombinase, generating circular mini-chromosomes with all the components of the donor and recipient DNA. Mini-chromosomes were delivered into E. coli and selected on medium containing kanamycin and chloramphenicol. Only vectors that successfully cre recombined and contained both selectable markers survived in the medium. Mini-chromosomes were extracted from bacteria and restriction digested to verify DNA composition and calculate centromere insert size (Table 7).

TABLE 7 Cre/Lox Recombined Mini-chromosomes for Brassica Brassica Centromere Centromere insert Mini-Chromosome Fragment (kbp) Donor Vector BB5R4-1 5 64 pCHR151 BB5R10-1 5 48 pCHR171A BB5R14-6 5 52 pCHR487 BB5R15-4 5 52 pCHR488 BB5R16-6 5 50 pCHR489 BB71R1-1 71 30 pCHR151 BB221R2-1 221 70 pCHR487 BB222R2-7 222 60 pCHR487 BB229R2-6 229 60 pCHR487 BB280R2-3 280 97 pCHR487 Mini-chromosome Construction by Restriction-Ligation

Mini-chromosomes were also constructed using standard cloning procedures. For example, a BAC containing a centromere fragment was digested with a restriction endonuclease that created sticky ends, as for example, but not limited to NotI, which was commonly used for this purpose. The digested DNA was then electrophoresed to purify the centromere fragment into a single band. The electrophoresis was carried out with either conventional agarose gel electrophoresis with a linear electric field, or CHEF gel electrophoresis using an electric field that switches its orientation in the course of the run. When the electrophoresis was complete, the centromere fragment was visualized by ethidium bromide staining and illumination under ultraviolet light. The band corresponding to centromere DNA was excised, and the DNA was purified from the gel using conventional method for gel-purifying DNA fragments from agarose gels. The purified fragment was then ligated with a vector fragment that contains a low-copy E. coli backbone (e.g. the F′ plasmid replicon) and one or more plant-expressed genes. The vector fragment was digested with a restriction endonuclease leaving compatible sticky ends to those present on the centromere fragment. Alternatively, both fragments may be blunt.

To achieve a high rate of insertion of the centromere fragment into the vector, the phosphate groups were removed from the ends of the vector molecule by treating this DNA molecule with phosphatase; this step prevented ligation of the vector molecule to itself or to other vector molecules. After ligating vector DNA and centromere fragment, the mini-chromosomes were delivered into E. coli and selected on medium containing antibiotics corresponding to the antibiotic-resistance genes present on the vector molecule (e.g. kanamycin and chloramphenicol). Mini-chromosomes are extracted from bacteria and restriction digested to verify DNA composition and calculate centromere insert size (Table 8).

TABLE 8 Restriction-Ligation Mini-chromosomes Brassica Centromere Centromere insert Mini-Chromosome Fragment (kbp) Donor Vector pCHR543 5R4-1 64 pCHR510 pCHR591 5R4-1 64 pCHR579 pCHR593 5R4-1 64 pCHR581 pCHR816 5R4-1 64 pCHR806 pCHR817 5R4-1 64 pCHR807 pCHR818 5R4-1 64 pCHR808 pCHR819 5R4-1 64 pCHR809 pCHR820 5R4-1 64 pCHR810 pCHR821 5R4-1 64 pCHR811 pCHR823 5R4-1 64 pCHR813 pCHR824 5R4-1 64 pCHR814 pCHR825 5R4-1 64 pCHR815 pCHR955 5R4-1 64 pCHR945 pCHR958 5R4-1 64 pCHR948 pCHR964 15R4-1 121 pCHR807 pCHR965 15R4-1 121 pCHR815 pCHR967 16R1-2 156 pCHR815 pCHR970 52R1-1 99 pCHR807 pCHR972 60R1-1 49 pCHR807 pCHR973 60R1-1 49 pCHR815 Cloning Vector

The vector, pBeloBAC11, is an E. coli plasmid cloning vector based on the F′ plasmid replicon of E. coli. The vector contained a chloramphenicol resistance gene for selection of the plasmid in bacteria, repE, sopA/B/and C for maintenance of the plasmid in bacteria, and a LoxP recombination site for specific cleavage by Cre recombinase. A description of all the genes contained within the vector and the location of the gene within the vector are set out in Table 9.

TABLE 9 pBeloBAC11 components Size (base Genetic Element pair) Location (bp) Details Bacterial 660  766-1425 Bacterial selectable Chloramphenicol (complementary) marker resistance ori2 67 2370-2436 F′ plasmid origin of replication from E. coli repE 755 2765-3520 mediation of replication complex at Ori2 (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopA 1166 4108-5274 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopB 971 5274-6245 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopC 474 6318-6791 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) cos 400 7050-7449 Lambda DNA recognition sequence for phage packaging LoxP 34 7467-7500 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984) Source of Coding Regions Used in Plant-Expressed Genes

The fluorescent reporter genes DsRed, and AmCyan were isolated from Athozoa species; and ZsYellow and ZsGreen were isolated from Zoanthus sp (Matz et. al. Nature Biotechnol. 1999 October; 17:969). These reporter genes express proteins that are homologous to Green Fluorescent Protein (GFP), which is a commonly used reporter gene in various biological systems, including plants. All fluorescent reporter genes were obtained from Clontech Corporation (Palo Alto, Calif.).

The selectable marker gene MerA is a mercuric ion reductase which converts toxic Hg²⁺ to less toxic metallic mercury. This gene was originally isolated from E. coli and then modified to accommodate improved expression in plants (Rugh et. al. PNAS 1996 93:318).

The selectable marker gene NPTII (neomycin phosphotransferase II) has been commonly used in plants as a selectable agent (Bevan et. al. Nature 1983 304:184). The original source of this gene is E. coli.

Donor Vectors Used to Construct Mini-Chromosomes Via Cre/Lox Recombinations

pCHR151

The plasmid pCHR151 was developed using the commercially available high copy number E. coli cloning vector pUC19 (Yanisch-Perron et al., (1985) Gene 33, 103-119). The plasmid backbone was modified with the bacterial kanamycin selectable marker for maintenance of the plasmid in bacterial hosts, a pair of complementary loxP sites and a polylinker that facilitated the modular assembly of several plant-expressed genes for expression in plant mini-chromosomes. Using standard cloning methods, plant-expressed gene cassettes were introduced into the modified pUC19 vector to construct pCHR151. This vector includes DsRed with a nuclear localization signal (Clontech Corporation, Palo Alto Calif.), which was regulated by the Arabidopsis UBQ10 promoter (At4g05320) and the Arabidopsis pyruvate kinase terminator (At5g52920). The vector also included the E. coli MerA gene regulated by the Arabidopsis thaliana ACT2 promoter and terminator. The vector also contains a high-copy E. coli replication origin and an ampicillin bacterial selectable marker. Mini-chromosome genetic elements within the pCHR151 vector are set out in Table 10.

Prior to using pCHR151 to construct plant mini-chromosomes, pCHR151 was digested with restriction endonucleases to linearize the pCHR151 plasmid and remove the high copy origin of replication and the bacterial ampicillin selectable marker, leaving loxP recombination sites on each end of the linear fragment. The resulting linearized vector was cre recombined in vitro to generate circular donor pCHR151 plasmids lacking a bacterial origin of replication and the ampicillin selectable marker. The donor pCHR151 construct was used to construct plant mini-chromosomes.

TABLE 10 Donor Components of pCHR151 Size Genetic Element (bp) Location (bp) Details Act2 promoter + 1482 7473-8954 The Arabidopsis thaliana intron (complementary) promoter Actin 2 plus natural intron. MerA 1695 5776-7470 Plant selectable marker (complementary) providing resistance to mercuric ions (Rugh et.al. PNAS 1996 93: 3182). Act2 800 4823-5622 Arabidopsis thaliana Actin terminator (complementary) 2 terminator. Bacterial 817 3825-4641 Bacterial kanamycin Kanamycin (complementary) selectable marker Pyruvate 332 3349-3680 Arabidopsis thaliana kinase Pyruvate kinase terminator terminator (At5g52920) DsRed2 + 780 2435-3214 Nuclear localized red NLS fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 2038  361-2398 Arabidopsis thaliana Promoter polyubiquitin promoter (At4g05320) LoxP 34 346-379 Recombination site for Cre and mediated recombination 9005-9038 (Arenski et. al 1983, Abremski et. al 1984)

pCHR171A

The vector pCHR171A vector was used to generate linear mini-chromosomes by introducing plant telomere sequences. The donor region of pCHR171A is identical to pCHR151 (described above) with the exception of two plant telomeric regions located on both sides of the bacterial kanamycin gene. pCHR171A was constructed using standard cloning methods. Similar to construction of pCHR151, the low copy bacterial backbone of pBeloBAC11 was used in place of the pUC19 high copy backbone to stabilize the addition of the highly repetitive plant telomeric sequences. The bacterial tetracycline gene replaced the pBeloBAC11 chloramphenicol gene for bacterial selection.

Naturally occurring plant telomeres are composed of a seven nucleotide repeat (TAAACCC). Plant telomeres were polymerized using standard PCR methods to generate approximately 800 base pair telomere arrays. The telomere sequences were ligated using standard methods on both sides of the bacterial kanamycin gene. Two unique I-PpoI homing endonuclease restriction sites were introduced between each telomere and the kanamycin gene for linearization of the final mini-chromosome construct. Mini-chromosome genetic elements within the pCHR171 vector are set out in Table 11 below.

TABLE 11 Donor Components of pCHR171A Size Genetic Element (base pair) Location (bp) Details Act2 promoter + intron 1482  97-1578 The Arabidopsis thaliana promoter Actin 2 plus natural intron. MerA 1695 1581-3275 Plant selectable marker providing resistance to mercuric ions (Rugh et.al. PNAS 1996 93: 3182). Act2 terminator 800 3429-4228 Arabidopsis thaliana Actin 2 terminator. Plant telomere 759 4277-5035 Plant telomere PCR based on plant consensus telomere sequence Bacterial Kanamycin 817 5211-6027 Bacterial kanamycin selectable marker Plant telomere 760 6161-6920 Plant telomere PCR based on plant consensus telomere sequence Pyruvate kinase 332 6968-7299 Arabidopsis thaliana Pyruvate terminator kinase terminator (At5g52920) DsRed2 + NLS 780 7434-8213 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 Promoter 2038  8250-10287 Arabidopsis thaliana polyubiquitin promoter (At4g05320) LoxP 34 47-80 and 10303-10336 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984)

To generate plant mini-chromosomes with pCHR171A, the vector was digested and cre treated using the same methods as described for pCHR151 to generate donor pCHR171A. Restriction digests of pCHR171A removed the low copy origin of replication and the bacterial tetracycline selectable marker, leaving loxP recombination sites on each end of the linear fragment. The resulting linearized vector was cre recombined in vitro to generate circular donor pCHR171A plasmids lacking a bacterial origin of replication and the tetracycline selectable marker.

Cre recombinase-mediated exchange was used to construct mini-chromosomes by combining the plant centromere fragments of pBeloBAC11 with the donor vector pCHR171A. The recipient BAC vector carrying the plant centromere fragment contained a loxP recombination site, facilitating the introduction of donor DNA via the action of cre recombinase. Using purified cre recombinase in vitro, BAC centromere recipients were combined with donor pCHR171A DNA, generating circular mini-chromosomes with all the components of the donor and recipient DNA. Mini-chromosomes were delivered into E. coli and selected on medium containing kanamycin and chloramphenicol. Only vectors that successfully cre recombined contained both selectable markers and were easily selected from non-recombined events. Mini-chromosomes were extracted from bacteria and restriction digested to verify DNA composition and calculate centromere insert size.

To generate linear mini-chromosomes constructed with donor pCHR171A, E. coli harboring the mini-chromosomes were grown in selective bacterial growth medium and purified using standard alkaline lysis procedures. Purified mini-chromosomes were restriction digested in vitro with homing endonuclease enzyme I-PpoI following standard restriction digest procedures. Linearization of the mini-chromosome results in the removal of the bacterial kanamycin gene cassette leaving plant telomeres flanking both ends of the linear mini-chromosome. Linear mini-chromosomes were ethanol precipitated and used for plant transformation.

Other Donor Vectors used via Cre/Lox Recombination

The pCHR487 mini-chromosome donor vector was also used to generate Brassica mini-chromosomes. In this vector, the Act2 promoter-MerA gene cassette of pCHR151 was replaced with the yeast TEF2 promoter from Saccharomyces cerevisiae and the plant kanamycin selectable marker NptII from E. coli. To enhance the stability of the NptII transcript, the Arabidopsis thaliana UBQ10 intron was inserted 5′ of the yeast TEF2 promoter and 3′ of the NptII gene. The UBQ10 intron is a naturally occurring component of the transcribed sequences from the Arabidopsis thaliana UBQ10 gene and was present in the UB10 promoter in pCHR151. Standard restriction digest and cloning methods were used to generate pCHR487. Construction of plant mini-chromosomes using pCHR487 was performed as described for pCHR151. As with pCHR151, the circular donor pCHR487 lacked a bacterial origin of replication and the bacterial ampicillin selectable marker. Mini-chromosome genetic elements within the pCHR487 vector are set out in Table 12.

TABLE 12 Donor Components of pCHR487 Size Genetic Element (base pair) Location (bp) Details UBQ10 promoter 2038 361-2398 Arabidopsis thaliana polyubiquitin promoter (At4g05320) DsRed2 + NLS 780 2435-3214 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Pyruvate kinase 332 3349-3680 Arabidopsis thaliana pyruvate terminator kinase terminator (At5g52920) Bacterial Kanamycin 817 3825-4641 Bacterial kanamycin selectable marker Act2 terminator 800 4823-5622 Arabidopsis thaliana Actin 2 terminator NptII 795 5685-6479 Neomycin phosphotransferase II plant selectable marker UBQ10 intron 359 6507-6865 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels TEF2 Promoter 2000 6880-8879 Saccharomyces cerevisiae translation elongation factor alpha promoter for expression of NptII LoxP 34 312-345 & 8898-8931 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984)

In the pCHR488 mini-chromosome donor vector, the yeast TEF2 promoter of pCHR487 was replaced with the yeast GPD1 promoter which drove the plant selectable marker NptII. The yeast GPD1 promoter was PCR amplified from Saccharomyces cerevisiae genomic DNA using standard PCR methods. Standard cloning methods were also used to replace the TEF2 promoter and insert the yeast GPD1 promoter. For construction of mini-chromosomes, donor pCHR488 was generated as described for pCHR151. As with pCHR151, the circular donor pCHR488 lacks a bacterial origin of replication and the bacterial ampicillin selectable marker. The donor pCHR488 construct was used to construct plant mini-chromosomes as described for pCHR151. Mini-chromosome genetic elements within the pCHR488 vector are set out in Table 13

TABLE 13 Donor Components of pCHR488 Size Genetic Element (base pair) Location (bp) Details UBQ10 promoter 2038  361-2398 Arabidopsis thaliana polyubiquitin promoter (At4g05320) DsRed2 + NLS 780 2435-3214 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Pyruvate kinase 332 3349-3680 Arabidopsis thaliana pyruvate terminator kinase terminator (At5g52920) Bacterial Kanamycin 817 3825-4641 Bacterial kanamycin selectable marker Act2 terminator 800 4823-5622 Arabidopsis thaliana Actin 2 terminator NptII 795 5685-6479 Neomycin phosphotransferase II plant selectable marker UBQ10 intron 359 6500-6859 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels GPD1 Promoter 2000 6880-8879 Saccharomyces cerevisiae glycerol- 3-phosphate dehydrogenase (NAD+) promoter for expression of NptII LoxP 34 312-345 & 8898-8931 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984)

In the pCHR489 mini-chromosome donor vector, the yeast TEF2 promoter of pCHR487 was replaced with the Drosophila melanogaster Grim fly promoter for driving the plant selectable marker NptII. The Grim fly promoter was PCR amplified from Drosophila melanogaster genomic DNA using standard PCR methods. Standard cloning methods were used to replace the TEF2 promoter in pCHR487 with the Grim fly promoter to generate pCHR489. For construction of mini-chromosomes, donor pCHR489 was generated as described for pCHR151. As with pCHR151, the circular donor pCHR489 lacks a bacterial origin of replication and the bacterial ampicillin selectable marker. The donor pCHR489 construct was used to construct plant mini-chromosomes as described for pCHR151. Mini-chromosome genetic elements within the pCHR489 vector are set out in Table 14.

TABLE 14 Donor Components of pCHR489 Size Genetic Element (base pair) Location (bp) Details UBQ10 promoter 2038  361-2398 Arabidopsis thaliana polyubiquitin promoter (At4g05320) DsRed2 + NLS 780 2435-3214 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Pyruvate kinase 332 3349-3680 Arabidopsis thaliana pyruvate terminator kinase terminator (At5g52920) Bacterial Kanamycin 817 3825-4641 Bacterial kanamycin selectable marker Act2 terminator 800 4823-5622 Arabidopsis thaliana Actin 2 terminator NptII 795 5685-6479 Neomycin phosphotransferase II plant selectable marker UBQ10 intron 359 6507-6865 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels Grim Fly Promoter 2191 6880-8879 PCR amplified promoter of grim (AKA BcDNA: RE28551) from Drosophila melanogaster LoxP 34 312-345 & 9081-9114 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984) Vectors Used to Construct Mini-Chromosomes Via Standard Cloning Methods:

pCHR510

As in pCHR151, pCHR510 contains DsRed with a nuclear localization signal and is regulated by the Arabidopsis UBQ10 promoter. The Arabidopsis pyruvate kinase terminator (At5g52920) was replaced by standard cloning procedures with the Arabidopsis thaliana triose phosphate isomerase terminator to prevent redundant use of the Arabidopsis pyruvate kinase terminator (At5g52920) in pCHR510. In addition, the E. coli MerA gene cassette was replaced with the plant selectable marker NptII regulated by the Drosophila melanogaster Grim fly promoter plus Arabidopsis UBQ10 intron and the Arabidopsis pyruvate kinase terminator (At5g52920). The vector also included a ZsGreen fluorescent gene (Clontech Corporation, Palo Alto Calif.) regulated by the Arabidopsis Act2 promoter plus naturally occurring intron and the Arabidopsis Act2 terminator. The high-copy E. coli backbone of pUC19 and ampicillin bacterial selectable marker were replaced with the low copy pBeloBAC11 backbone with the bacterial streptomycin resistance gene replacing the chloramphenicol resistance gene. An Arabidopsis thaliana ST11 sub-telomeric fragment was introduced upstream of the Grim fly promoter to isolate the Grim fly promoter from possible promoter silencing when a centromere fragment was ligated into the donor vector. Mini-chromosome genetic elements within the pCHR510 vector are set out in Table 15 below.

TABLE 15 pCHR510 DNA donor components Size (base Genetic Element pairs) Location (bp) Details Bacterial 10111 16912-17922 Bacterial selectable marker streptomycin resistance ori2 67 19158-19224 F′ plasmid origin of replication from E. coli repE 755 19553-20308 mediation of replication complex at Ori2 (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopA 1166 20896-22062 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopB 971 22062-23033 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopC 517 23106-23623 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) LoxP 34 26-59 and Recombination site for Cre 16212-16245 mediated recombination (Arenski et. al 1983, Abremski et. al 1984) ST11 subtelomeric 4682  69-4750 Arabidopsis thaliana DNA (complementary) subtelomenic DNA from Chromosome 5 Grim Promoter 2187 4766-6956 PCR amplified Drosophila melanogaster Grim gene promoter for expression of NptII gene in plants. UBQ10 intron 359 6963-7322 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels. NptII 795 7350-8144 Neomycin phosphotransferase II plant selectable marker Pyruvate kinase 332 8212-8543 Arabidopsis thaliana Pyruvate terminator kinase terminator (At5g52920) Bacterial 817 8731-9547 Bacterial kanamycin selectable Kanamycin marker Act2 promoter + intron 1482  9690-11171 The Arabidopsis thaliana promoter Actin 2 plus natural intron. ZsGreen 695 11195-11890 Matz et. al. Nature Biotechnol. 1999 Oct.; 17: 969 Act2 terminator 800 11931-12730 Arabidopsis thaliana Actin2 gene terminator. Triose phosphate 450 12759-13208 Arabidopsis thaliana Triose isomerase (complementary) phosphate isomerase gene terminator DsRed2 + NLS 780 13343-14122 Nuclear localized red (complementary) fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 Promoter 2038 14159-16196 Arabidopsis thaliana (complementary) polyubiquitin promoter (At4g05320)

To construct mini-chromosomes using pCHR510, the vector was linearized using standard restriction digestion procedures. The Brassica centromere fragment from mini-chromosome BB5R4-1 was restriction digested using Not I and ligated into pCHR510 using standard cloning procedures to generate the mini-chromosome pCHR543. Mini-chromosomes were delivered into E. coli and grown in selective medium. Mini-chromosomes were extracted from bacteria and restriction digested to verify DNA composition and verify centromere insert size.

pCHR579

The pCHR579 mini-chromosome donor vector was constructed using the same method to construct the pCHR510, without replacing the bacterial chloramphenicol gene in the low copy pBeloBAC11 backbone. Using standard cloning methods the bacterial kanamycin gene was replaced with a bacterial kanamycin selectable marker surrounded by two plant telomere sequences and two unique 1-PpoI homing endonuclease sequences as described in pCHR171A. Mini-chromosomes using pCHR579 were constructed as described for pCHR510 using BB5R4-1 centromeric DNA to construct pCHR591. pCHR591 was linearized as described for mini-chromosomes described above for pCHR171A. Mini-chromosome genetic elements within the pCHR579 vector are set out in Table 16 below.

TABLE 16 pCHR579 DNA donor components Size (base Genetic Element pairs) Location (bp) Details Bacterial 660 18022-18681 Bacterial selectable chloramphenicol marker resistance ori2 67 19685-19751 F factor origin of replication from E. coli repE 755 20080-20835 mediation of replication complex at Ori2 (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopA 1166 214230-22589 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopB 971 22589-23560 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopC 517 23633-24150 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) LoxP 34 26-59 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984) ST11 sub-telomeric 4682  69-4750 Arabidopsis thaliana DNA (complementary) subtelomeric DNA from Chromosome 5 Grim Fly Promoter 2187 4766-6956 PCR amplified Drosophila melanogaster Grim gene promoter for expression of NptII gene in plants. UBQ10 intron 359 6963-7322 PCR amplified Arabidopsis thaliana intron from UBQ10 promoter (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels. NptII 795 7350-8144 Kanamycin plant selectable marker Pyruvate kinase 332 8212-8543 Arabidopsis thaliana terminator Pyruvate kinase terminator (At5g52920) Plant telomere 759 8598-9356 Plant telomere PCR based on plant consensus telomere sequence Bacterial 817  9532-10348 Bacterial kanamycin Kanamycin selectable marker Plant telomere 759 10482-11241 Plant telomere PCR based on plant consensus telomere sequence Act2 promoter + 1482 11287-12768 The Arabidopsis thaliana intron promoter Actin 2 plus natural intron. ZsGreen 695 12792-13487 Matz et.al. Nature Biotechnol. 1999 Oct.; 17: 969 Act2 terminator 800 13528-14327 Arabidopsis thaliana Actin2 gene terminator. Triose phosphate 450 14356-14805 Arabidopsis thaliana isomerase (complementary) Triose phosphate isomerase gene terminator DsRed2 + NLS 780 14940-15719 Nuclear localized red (complementary) fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 Promoter 2038 15756-17793 Arabidopsis thaliana (complementary) polyubiquitin promoter (At4g05320)

pCHR581

The pCHR581 mini-chromosome donor vector was constructed using standard cloning procedures. The vector was constructed as pCHR579 with no ST11 sub-telomeric DNA. Mini-chromosome genetic elements within the pCHR581 vector are set out in Table 17 below.

ST9 is an Arabidopsis thaliana sub-telomeric sequence from centromere 5 (bases 3708-195 (3513 bp); Database: ATH1_chr5.1con), which was amplified with the following oligo nucleotides: CHHZ-199 (GGTGGTCGGCCGGAGCACAA GCGGGCCAAGCCCATGCTTG; SEQ ID NO: 29) and CHHZ-202 (GGTGGTCGGCCGCAGGTTGCATATGAATCTTTA ACTGACAG; SEQ ID NO: 30). ST10 is an Arabidopsis thaliana sub-telomeric sequence from centromere 5 (bases 195-3708 (3513 bp); Database: ATH1_chr5.1con), which was amplified with the following oligo nucleotides: CHHZ-200 (GGTGGTCGGCCGCGAGCACAAGCGGGCCAAGCCCATGCTTG; SEQ ID NO: 31) and CHHZ-201 (GGTGGTCGGCCGTCAGGTTGCATATGAATCTT TAACTGACAG: SEQ ID NO: 32). ST11 is an Arabidopsis thaliana sub-telomeric sequence from centromere 5 (bases 26,987,774-26,992,453 (4681 bp); Database: ATH1_chr5.1 con), which was amplified with the following oligo nucleotides: CHHZ-203 (GGTGGTCGGCCGTCGTCGGCACTTGGCAGCGAAATCTCC; SEQ ID NO: 33) and CHHZ-206 (GGTGGTCGGCCGCATTATCATATAATTATGTTT TGCTGCTTC: SEQ ID NO: 34). ST12 is an Arabidopsis thaliana sub-telomeric sequence from centromere 5 (bases 26,992,453-26,987,774 (4681 bp); Database: ATH1_chr5.1con), which was amplified with the following oligo nucleotides: CHHZ-204 (GGTGGTCGGCCGCGTCGGCACTTGGCAGCGAAATCTCC; SEQ ID NO: 35) and CHHZ-205 (GGTGGTCGGCCGATTATCATATAATTATGT TTTGCTGCTTC: SEQ ID NO: 36). These sub-telomeric sequences were included in the pCRR581 vector.

TABLE 17 pCHR581 DNA donor components Size (base Genetic Element pairs) Location (bp) Details Bacterial 660 13333-13992 Bacterial selectable marker chloramphenicol resistance ori2 67 14996-15062 F′ plasmid origin of replication from E. coli repE 755 15391-16146 mediation of replication complex at Ori2 (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopA 1166 16734-17900 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopB 971 17900-18871 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopC 517 18944-19461 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) LoxP 34 26-59 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984) Grim Promoter 2187  77-2267 PCR amplified Drosophila melanogaster Grim gene promoter for expression of NptII gene in plants UBQ10 intron 359 2274-2633 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels. NptII 795 2661-3455 Neomycin phosphotransferase II plant selectable marker Pyruvate kinase 332 3523-3854 Arabidopsis thaliana Pyruvate terminator kinase terminator (At5g52920) Plant telomere 759 3909-4667 Plant telomere PCR based on plant consensus telomere sequence Bacterial Kanamycin 817 4843-5659 Bacterial kanamycin selectable marker Plant telomere 759 5793-6552 Plant telomere PCR based on plant consensus telomere sequence Act2 promoter + intron 1482 6598-8079 The Arabidopsis thaliana promoter Actin 2 plus natural intron. ZsGreen 695 8103-8798 Matz et. al. Nature Biotechnol. 1999 Oct.; 17: 969 Act2 terminator 800 8839-9638 Arabidopsis thaliana Actin2 gene terminator. Triose phosphate 450  9667-10116 Arabidopsis thaliana Triose isomerase (complementary) phosphate isomerase gene terminator DsRed2 + NLS 780 10251-11030 Nuclear localized red (complementary) fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 Promoter 2038 11067-13104 Arabidopsis thaliana (complementary) polyubiquitin promoter (At4g05320)

pCHR806

The pCHR806 mini-chromosome vector was constructed using standard cloning procedures. The vector was composed similarly to that of pCHR510 using the pBeloBAC11 low copy backbone containing the bacterial chloramphenicol gene and without the addition of the ST11 sub-telomeric DNA. An additional plant gene cassette was introduced containing the Anemonia sp. cyan fluorescence (AmCyan) gene regulated by the tomato Lat52 promoter and terminator. Mini-chromosome genetic elements within the pCHR806 vector are set out in Table 18.

TABLE 18 pCHR806 Genetic Element Size (base pairs) Location (bp) Details Bacterial 660 13372-14031 Bacterial selectable marker chloramphenicol resistance ori2 67 15035-15101 F′ plasmid origin of replication from E. coli repE 755 15430-16185 mediation of replication complex at Ori2 (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopA 1166 16773-17939 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopB 971 17939-18910 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopC 517 18983-19500 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) LoxP 34 26-59 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984) Grim Promoter 2187  77-2267 PCR amplified Drosophila melanogaster Grim gene promoter for expression of NptII gene in plants. UBQ10 intron 359 2274-2633 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels. NptII 795 2661-3455 Neomycin phosphotransferase II plant selectable marker Pyruvate kinase 332 Arabidopsis thaliana terminator Pyruvate kinase terminator (At5g52920) Lat52 terminator 200 3883-4082 Tomato Lat52 terminator (complementary) AmCyan 690 4123-4812 Visible cyan fluorescent (complementary) protein from Anemonia majano (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Tomato Lat52 668 4836-5503 Tomato Lat52 promoter promoter (complementary) Bacterial Kanamycin 817 5678-6494 Bacterial kanamycin selectable marker Act2 promoter + intron 1482 6637-8118 The Arabidopsis thaliana promoter Actin 2 plus natural intron. ZsGreen 695 8142-8837 Matz et. al. Nature Biotechnol. 1999 Oct.; 17: 969 Act2 terminator 800 8878-9677 Arabidopsis thaliana Actin2 gene terminator. Triose phosphate 450  9706-10155 Arabidopsis thaliana Triose isomerase phosphate isomerase gene terminator DsRed2 + NLS 780 10290-11069 Nuclear localized red (complementary) fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 Promoter 2038 11106-13143 Arabidopsis thaliana (complementary) polyubiquitin promoter (At4g05320)

pCHR807

The pCHR807 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR806. The vector was composed similar to that of pCHR510 using the pBelloBAC11 low copy backbone containing the bacterial chloramphenicol gene and without the addition of the ST11 sub-telomeric DNA. An additional plant gene cassette was introduced containing the Zoanthus sp. yellow fluorescent gene (ZsYellow) regulated by the tomato Lat52 promoter and terminator. Mini-chromosome genetic elements within the pCHR807 vector are set out in Table 19.

TABLE 19 pCHR807 DNA donor components Size (base Genetic Element pairs) Location (bp) Details Bacterial 660 13378-14037 Bacterial selectable marker chloramphenicol resistance ori2 67 15041-15107 F′ plasmid origin of replication from E. coli repE 755 15436-16191 mediation of replication complex at Ori2 (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopA 1166 16779-17945 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopB 971 17945-18916 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopC 517 18989-19506 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) LoxP 34 26-59 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984) Grim Promoter 2187  77-2267 PCR amplified Drosophila melanogaster Grim gene promoter for expression of NptII gene in plants. UBQ10 intron 359 2274-2633 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels. NptII 795 2661-3455 Neomycin phosphotransferase II plant selectable marker Pyruvate kinase 332 3523-2854 Arabidopsis thaliana Pyruvate terminator kinase terminator (At5g52920) Lat52 terminator 200 3883-4082 Tomato Lat52 terminator (complementary) ZsYellow 696 4123-4818 Visible yellow fluorescent (complementary) protein from Zoanthus sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Tomato Lat52 668 4842-5509 Tomato Lat52 promoter promoter Bacterial 817 5684-6500 Bacterial kanamycin Kanamycin selectable marker Act2 promoter + intron 1482 6643-8124 The Arabidopsis thaliana promoter Actin 2 plus natural intron. ZsGreen 695 8148-8843 Matz et. al. Nature Biotechnol. 1999 Oct.; 17: 969 Act2 terminator 800 8884-9683 Arabidopsis thaliana Actin2 gene terminator. Triose phosphate 450  9712-10161 Arabidopsis thaliana Triose isomerase phosphate isomerase gene terminator DsRed2 + NLS 780 10296-11075 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 Promoter 2038 11112-13149 Arabidopsis thaliana polyubiquitin promoter (At4g05320)

pCHR808

The pCHR808 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR806, but with the addition of the Arabidopsis thaliana ST9 sub-telomeric DNA. The ST9 sub-telomeric fragment was introduced upstream of the Grim fly promoter to isolate the Grim fly promoter from possible promoter silencing when a centromere fragment is ligated into the donor vector. Mini-chromosome genetic elements within the pCHR808 vector are set out in Table 20.

TABLE 20 pCHR808 DNA donor components Size (base Genetic Element pairs) Location (bp) Details Bacterial 660 16892-17551 Bacterial selectable chloramphenicol marker resistance ori2 67 18555-18621 F′ plasmid origin of replication from E. coli repE 755 18950-19705 mediation of replication complex at Ori2 (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopA 1166 20293-21459 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopB 971 21459-22430 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopC 517 22503-23020 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) LoxP 34 26-59 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984) ST9 subtelomeric 3513  69-3581 Arabidopsis thaliana DNA subtelomeric DNA from Chromosome 5 Grim Promoter 2187 3597-5787 PCR amplified Drosophila melanogaster Grim gene promoter for expression of NptII gene in plants. UBQ10 intron 359 5794-6153 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels. NptII 795 6181-6975 Neomycin phosphotransferase II plant selectable marker Pyruvate kinase 332 7043-7374 Arabidopsis thaliana terminator Pyruvate kinase terminator (At5g52920) Lat52 terminator 200 7403-7602 Tomato Lat52 terminator (complementary) AmCyan 690 7643-8332 Visible cyan fluorescent protein from Anemonia majano (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Tomato Lat52 668 8356-9023 Tomato Lat52 promoter promoter (complementary) Bacterial 817  9198-10014 Bacterial kanamycin Kanamycin selectable marker Act2 promoter + 1482 10157-11638 The Arabidopsis thaliana intron promoter Actin 2 plus natural intron. ZsGreen 695 11662-12357 Matz et.al. Nature Biotechnol. 1999 Oct.; 17: 969 Act2 terminator 800 12398-13197 Arabidopsis thaliana Actin2 gene terminator. Triose phosphate 450 13226-13675 Arabidopsis thaliana isomerase Triose phosphate isomerase gene terminator DsRed2 + NLS 780 13810-14589 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 Promoter 2038 14626-16663 Arabidopsis thaliana polyubiquitin promoter (At4g05320)

pCHR945

The pCHR945 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR807 with the replacement of the bacterial kanamycin gene with a bacterial kanamycin selectable marker gene surrounded by two plant telomere sequences and two unique I-Ppo I homing endonuclease sequences as described in pCHR171A. Mini-chromosomes using pCHR945 were constructed as described for pCHR510 using BB5R4-1 centromeric DNA to construct pCHR955. pCHR955 was linearized as described for mini-chromosomes constructed with pCHR171A. Mini-chromosome genetic elements within the pCHR845 vector are set out in Table 21.

TABLE 21 pCHR945 DNA donor components Size (base Genetic Element pairs) Location (bp) Details Bacterial chloramphenicol 660 14992-15651 Bacterial selectable marker resistance ori2 67 16655-16721 F′ plasmid origin of replication from E. coli repE 755 17050-17805 mediation of replication complex at Ori2 (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopA 1166 18393-19559 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopB 971 19559-20530 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) SopC 517 20603-21120 partition of plasmid to bacterial daughter cells (Mori, H et. al, J Mol Biol. 1986 Nov. 5; 192(1): 1-15) LoxP 34 26-59 Recombination site for Cre mediated recombination (Arenski et. al 1983, Abremski et. al 1984) Grim Promoter 2187  77-2267 PCR amplified Drosophila melanogaster Grim gene promoter for expression of NptII gene in plants. UBQ10 intron 359 2274-2633 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels. NptII 795 2661-3455 Neomycin phosphotransferase II plant selectable marker Pyruvate kinase terminator 332 3523-3854 Arabidopsis thaliana Pyruvate kinase terminator (At5g52920) Lat52 terminator 200 3883-4082 Tomato Lat52 terminator (complementary) ZsYellow 696 4123-4818 Visible yellow fluorescent (complementary) protein from Zoanthus sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Tomato Lat52 promoter 668 4842-5509 Tomato Lat52 promoter (complementary) Plant telomere 759 5568-6326 Plant telomere PCR based on plant consensus telomere sequence Bacterial Kanamycin 817 6502-7318 Bacterial kanamycin selectable marker Plant telomere 759 7452-8211 Plant telomere PCR based on plant consensus telomere sequence Act2 promoter + intron 1482 8257-9738 The Arabidopsis thaliana promoter Actin 2 plus natural intron. ZsGreen 695  9762-10457 Matz et.al. Nature Biotechnol. 1999 Oct.; 17: 969 Act2 terminator 800 10498-11297 Arabidopsis thaliana Actin2 gene terminator. Triose phosphate isomerase 450 11326-11775 Arabidopsis thaliana Triose terminator (complementary) phosphate isomerase gene terminator DsRed2 + NLS 780 11910-12689 Nuclear localized red (complementary) fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). UBQ10 Promoter 2038 12726-14763 Arabidopsis thaliana (complementary) polyubiquitin promoter (At4g05320)

Other Vectors

The pCHR809 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR807, but with the addition of the Arabidopsis thaliana ST9 sub-telomeric DNA. The ST9 sub-telomeric fragment was introduced upstream of the Grim fly promoter to isolate the Grim fly promoter from possible promoter silencing when a centromere fragment was ligated into the donor vector.

The pCHR810 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR806, but with the addition of the Arabidopsis thaliana ST10 sub-telomeric DNA. The ST10 sub-telomeric fragment was introduced upstream of the Grim fly promoter to isolate the Grim fly promoter from possible promoter silencing when a centromere fragment was ligated into the donor vector.

The pCHR811 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR807, but with the addition of the Arabidopsis thaliana ST10 sub-telomeric DNA. The ST10 sub-telomeric fragment was introduced upstream of the Grim fly promoter to isolate the Grim fly promoter from possible promoter silencing when a centromere fragment was ligated into the donor vector.

The pCHR813 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR807, but with the addition of the Arabidopsis thaliana ST11 sub-telomeric DNA. The ST11 sub-telomeric fragment was introduced upstream of the Grim fly promoter to isolate the Grim fly promoter from possible promoter silencing when a centromere fragment was ligated into the donor vector.

The pCHR814 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR806, but with the addition of the Arabidopsis thaliana STI 1 sub-telomeric DNA. The ST12 sub-telomeric fragment was introduced upstream of the Grim fly promoter to isolate the Grim fly promoter from possible promoter silencing when a centromere fragment was ligated into the donor vector.

The pCHR815 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR807, but with the addition of the Arabidopsis thaliana ST11 sub-telomeric DNA. The ST12 sub-telomeric fragment was introduced upstream of the Grim fly promoter to isolate the Grim fly promoter from possible promoter silencing when a centromere fragment was ligated into the donor vector.

The pCHR948 mini-chromosome donor vector was constructed using standard cloning procedures and is identical to pCHR810 with the replacement of the bacterial kanamycin gene with a bacterial kanamycin selectable marker gene surrounded by two plant telomere sequences and two unique I-Ppo I homing endonuclease sequences as described in pCHR171A. Mini-chromosomes using pCHR948 were constructed as described for pCHR510 using BB5R4-1 centromeric DNA. pCHR958 was linearized as described for mini-chromosomes constructed with pCHR171A.

Example 3 Mini-Chromosome Delivery into Brassica Cells

Various methods may be used to deliver DNA into plant cells. These include biological methods, such as Agrobacterium and viruses, physical methods such as biolistic particle bombardment and silicon carbide whiskers, electrical methods such as electroporation, and chemical methods such as the use of poly-ethylene glycol and other compounds known to stimulate DNA uptake into cells. Agrobacterium and biolistic particle bombardment have been the methods that have found most widespread use in plant biotechnology. See, e.g., Broothaerts, et. al. Nature 433: 629-633, 2005.

Biolistic Particle Delivery of Mini-Chromosomes

A biolistic delivery method using wet gold particles kept in an aqueous DNA suspension was adapted from the teachings of Milahe and Miller (Biotechniques 16: 924-931, 1994) and used to transform B. oleracea (Broccoli) cells. To prepare the wet gold particles for bombardment, 1.0 μm gold particles were washed by mixing with 100% ethanol on a vortex followed by spinning the particles in a microfuge at 4000 rpm in order to remove supernatant. Subsequently, the gold particles were washed with sterile distilled water three times, followed by spinning in a microfuge to remove supernatant. The washed gold particles were resuspend in sterile distilled water at a final concentration of 90 mg/ml and stored at 4° C. until use. For bombardment, the gold particle suspension (90 mg/ml) was then mixed rapidly with 1 μg/μl DNA solution (in dH₂O or TE), 2.5M CaCl₂, and 1M spermidine. When two or more plasmids were contained within the DNA solution, equal amounts of each plasmids was added to the gold suspension.

To prepare explant tissues for DNA delivery, three days prior to bombardment, an internode of the Brassica plant (Broccoli) were cut. The internode explant was cut longitudinally with a scalpel to cut a thin slice (⅙-¼ of the internode) off one side of the explant. The prepared internodes were placed wound side down on Petri dishes with regeneration media. The Petri dishes were wrapped with tape and placed wound side up under the light. The explants grew for 3 days prior to bombardment.

For bombardment of Brassica suspension cells, the cells were harvested by centrifugation (1200 rpm for 2 minutes) on the day of bombardment. The cells were plated onto 50 mm circular polyester screen cloth disks placed on petri plates with solid medium. The solid medium used was the same medium that the cells are normally grown in (MS salts, Gamborg's vitamins, 3% sucrose, 2 mg/liter 2,4D (2,4-Dichlorophenoxyacetic acid), 0.5 mM MES pH 5.8+(solid medium only), plus 0.26% gelrite, or 0.6% tissue culture agar, added before autoclaving. Approximately 1.5 ml packed cells were placed on each filter disk, and dispersed uniformly into a very even spot approximately 1 inch in diameter.

Bombardment of the cells was carried out in the BioRad PDS-1000/He Biolistic Particle Delivery System (BioRad). The DNA/gold suspension was resuspended and immediately inserted onto the grid of the filter holder. A 50 mm circular polyester screen cloth disk containing the cells was placed into a fresh 60 mm petri dish and the cells were covered with a 10×10 cm square of sterile nylon or Dacron chiffon netting. The metal cylinder was inserted into the petri dish and used to push the netting down to the bottom of the dish. This weight prevented the cells from being dislodged from the plate during bombardment. The petri dish containing the cells was then placed onto the sample holder, and positioned in the sample chamber of the gene gun and bombarded with the DNA/gold suspension. After the bombardment, the cells were scraped off the filter circle in the petri dish containing solid medium with a sterile spatula and transferred to fresh medium in a 125 ml blue-capped glass bottle. The bottles were transferred onto a shaker and grown while shaking at 150 rpm.

A biolistic delivery method using dry gold particles was also carried out to deliver mini-chromosomes to Brassica cells. For this method, 1.0 or 0.6μ gold particles were washed in 70% ethanol with vigorous shaking on a vortex for 3 to 5 minutes, followed by an soaking in 70% ethanol for 15 minutes. The gold particles were spun in a microfuge to remove the supernatant and washed three times in sterile distilled water. The gold particles were suspended in 50% glycerol at a concentration of 60 mg/ml and stored at 4° C. For bombardment, the dry gold particles were resuspended on a vortex for 5 minutes to disrupt agglomerated particles. Subsequently, the dry gold particles were mixed rapidly with DNA, 2.5M CaCl₂ and 0.2M spermidine in a siliconized, sterile eppendorf tube. The sample was allowed to settle for 1 minute and then spun in a microfuge for 10 seconds to remove supernatant. Subsequently, the DNA/gold particles were washed once with 70% ethanol, followed by two washed in 100% ethanol. A portion of the DNA/gold mixture was evenly placed on a macrocarrier. The macrocarrier was then placed in the BioRad PDS-1000/He Biolistic Particle Delivery System, and the bombardment was done at rupture disk pressures ranging from 450 psi to 2,200 psi. The dry biolistic method did not result in the generation of adchromosomal plants or cell lines.

Example 4 Selection of Brassica Cell Clones Stably Containing Mini-chromosome DNA Use of Visible Marker Genes

The presence of visible marker genes allowed for visual selection of Brassica cells stably containing mini-chromosome DNA because any adchromosomal cells or cell clusters were readily identified by virtue of fluorescent protein expression.

Transient assays were used to test mini-chromosomes for their ability to become established in cells following DNA delivery, and for their ability to be inherited in mitotic cell divisions. Expression of a visible marker encoded by a gene present on the mini-chromosome, such as a fluorescent protein gene, is used to detect mini-chromosome presence in the cell, and to follow mitotic inheritance of the mini-chromosome. In this assay, mini-chromosomes were delivered to Brassica cells of a population that is undergoing cell division, in this case Brassica suspension cells grown in liquid culture.

After DNA delivery, the cell population was monitored for fluorescent protein expression over the course of one to several weeks. Mini-chromosomes containing active centromeres were observed through the formation of fluorescent cell clusters, which were derived from a single progenitor cell that had divide and passed the mini-chromosomes to its daughter cells. Accordingly, single fluorescent cells and clusters of fluorescent cells of various sizes were scored in the growing cell population after DNA delivery. A total of 25 Brassica mini-chromosomes (see Table 23), constructed using the cre-lox assembly process, were tested in this manner in several different Brassica cell lines. A number of mini-chromosomes showed indications of stable mitotic inheritance in this assay and are listed in Table 22; in addition several stable cell lines were obtained from suspension cell lines following the delivery of the same mini-chromosomes; these are also listed in Table 22.

TABLE 22 Preferred Brassica BACs, centromeres (CEN), and mini-chromosomes (MC) based upon transient expression assays and generation of stable Brassica cell lines # of times # of Stable tested in positive BAC CEN MC clones transient transient Number Number Number BAC Class generated deliveries deliveries BB5 BB5R4-1 BB5R4-1 Hi CANREP, 7 3 2 Meth BB16 BB16R1-2 BB16R1-2 Hi CANREP, 0 2 1 Meth (Hpa) BB16R1-3 BB16R1-3 1 1 1 BB18 BB18R1-2 BB18R1-2 Hi CANREP, 1 1 1 Meth (Hpa) BB18R2-3 BB18R2-3 1 4 2 BB38 BB38R1-3 BB38R1-3 Hi CANREP 0 4 3 only BB47 BB47R1-2 BB47R1-2 Hi CANREP, 0 4 2 Meth (Hpa) BB60 BB60R1-1 BB60R1-1 Hi CANREP, 1 3 3 Meth (Hpa) BB63 BB63R1-1 BB63R1-1 Hi CANREP, 1 5 4 Meth (Hpa) BB70 BB70R1-3 BB70R1-3 Hi CANREP, 0 4 2 Moderate Meth BB71 BB71R1-3 BB71R1-1 Hi CANREP, 0 2 2 Meth (Sau) BB76 BB76R1-3 BB76R1-3 Hi CANREP, 0 5 4 Moderate Meth BB104 BB104R1-2 BB104R1-2 Hi CANREP, 1 3 3 Moderate Meth Manipulation of Adchromosomal Tissue to Homogeneity

After identifying clusters of fluorescent cells in bombarded suspension cell cultures, physical manipulations were carried out to allow for the preferential expansion of cells harboring the delivered genes. Non-fluorescent tissue surrounding the fluorescent clusters was trimmed to avoid overgrowth of fluorescent cells by non-fluorescent ones, while retaining a minimum tissue size capable of rapid growth. These manipulations were performed under sterile conditions with the use of a fluorescence stereomicroscope that allows for visualization of the fluorescent cells and cell clumps in the larger pieces of tissue. In between the mechanical purification steps, the tissue was allowed growth on appropriate media, either in the presence or absence of selection. Over time, a pure population of fluorescent cells was obtained.

Example 5 Regeneration of Brassica Plants from Adchromosomal Cell Clones

A total of 28 Brassica mini-chromosomes were used in stable transformation to successfully regenerate transchromosomal broccoli plants that are listed in Table 23. These Brassica mini-chromosomes represent candidate Brassica centromere sequences for the delivery and transmission of stable Brassica mini-chromosomes. B. oleracea plant (broccoli) regeneration was achieved by cultivating pieces of sterile plant tissue (explants) on medium containing plant growth activators (auxins, cytokinins and other compounds) that induce embryogenesis or shoot formation. Particularly, Brassica tissue proliferation was carried out with a medium containing high cytokinin regeneration medium (Murashige and Skooge salts, MES, sucrose, gelrite, Gamborg vitamins, 6-benzylaminopurine hydrochloride, non-essential amino acids, thidiazuron (TDZ) and silver nitrate, pH 5.7) through all culturing phases.

TABLE 23 In Growth size size Room # of of # # PCR³ RT³ Western³ Centromere MC cofig genes #explants⁵ cen MC events plants visual² # events # events # events BB15R4-1 964-4 O-O 4 77 60 80 1 1 √ 1 0 1 BB15R4-1 965-1 O-O 4 93 55 80 1 2 √ 1 0 1 BB16R1-2 967-1 O-O 4 105 55 60 1 1 √ 0 0 1 BB221 BB221R2-1 O-O 2 78 59 70 1 2 √ 0 0 1 BB222 BB222R2-7 O-O 2 102 49 60 1 2 √ 1 0 0 BB229 BB229R2-6 O-O 2 118 49 60 3 8 √ 2 0 1 BB280 BB280R2-3 O-O 2 79 86 97 3 6 √ 2 0 3 BB5 BB5R10-1 I-I 2 337 48 65 1 1 √ 1 0 0 BB5 BB5R14-6 O-O 2 213 52 68 1 1 √ 1 0 0 BB5 BB5R15-4 O-O 2 144 52 68 1 2 √ 1 0 0 BB5 BB5R16-6 O-O 2 152 50 66 2 6 √ 1 1 1 BB5R4-1 543-6 O-O 3 101 50 74 2 4 √ 1 0 0 BB5R4-1 591-1 I-O 3 76 50 75 1 2 √ 1 0 0 BB5R4-1 591-1L I-I 3 207 50 73 2 4 √ 2 1 1 BB5R4-1 593-3L I-I 3 78 50 69 1 4 √ 1 1 1 BB5R4-1 593-4L I-I 3 82 50 69 1 3 √ 1 1 1 BB5 BB5R4-1 O-O 2 564 50 61 7 46 √ 7 6 6 BB5R4-1 816-2 O-O 4 107 50 70 2 5 √ 2 1 1 BB5R4-1 817-1 O-O 4 143 50 70 2 16 √ 2 2 2 BB5R4-1 818-1 O-O 4 78 50 73 1 1 √ 1 0 0 BB5R4-1 819-1 O-O 4 117 50 73 4 14 √ 4 4 4 BB5R4-1 820-1 O-O 4 406 50 73 2 3 √ 2 0 1 BB5R4-1 823-2 O-O 4 50 50 75 3 16 √ 3 0 3 BB5R4-1 824-9 O-O 4 129 50 75 2 4 √ 2 2 2 BB5R4-1 825-1 O-O 4 168 50 75 1 1 √ 0 0 1 BB5R4-1 958-2L I-I 4 169 50 74 1 1 √ 1 0 1 BB60R1-1 972-5 O-O 4 123 60 80 1 2 √ 1 0 1 BB71 BB71R1-1 O-O 2 162 24 35 1 3 √ 1 1 1 integrative 489 O-O 2 306 0 11 1 1 √ 1 1 1 SB38R2-2 986-1 O-O 2 61 63 83 3 5 √ 3 0 3 167

After bombardment, explants were returned to the high cytokinin regeneration medium with the wound side down on the plate. The explants were transferred to selection medium (regeneration medium containing 150 μM HgCl₂ or 100 mg/L of kanamycin) three days after bombardment with wound side up. The explants were visually screened under a fluorescent dissecting microscope for red fluorescent cluster formation 10 days after selection was started. In addition to facilitating the transient assays, the use of fluorescent protein expression allowed for the use of sub-killing concentrations of selective agent during growth of plant tissue on selective medium. This flexibility allowed for the use of a wider range of antibiotic concentrations than possible in the absence of a visible marker gene, without having to consider the amount of background growth observed in wild type plant tissue. Fluorescent cell clusters could be visually identified after one to several weeks of growth on selective media. Clusters with some unmodified surrounding explant tissue were carved out and placed on medium containing 50 μM HgCl₂ or 50 mg/L of kanamycin.

The subcultures were continued on selection medium and the non-modified tissues were parsed out from the clusters every week for a month. Once the clusters were approximately 3 mm in size, they were cultured on regeneration medium without any Hg or kanamycin in order to induce shoot regeneration. Subsequently, shoot primordia were transferred to seed germination medium for enlargement and expansion. Once the shoots elongated and developed about 2-4 leaves, the shoots with the leaves were cut off for rooting in rooting medium (MS salts, sucrose, 0.7% tissue culture agar and non-essential amino acids, pH 5.7). Once the shoots developed good root systems, they were potted and transferred to a plant growth facility.

Example 6 Regeneration of B. napus (Canola) Plants Modified with Mini-chromosome DNA

The biolistic delivery method using dry gold particles, described in example 3, was used to deliver mini-chromosomes to B. napus hypocotyl sections for the purpose of regenerating modified B. napus (hereinafter “canola”) plants. The canola hypocotyls were modified with mini-chromosomes generated with Brassica centromere inserts described in Example 1 using the vectors described in Example 1.

Canola seeds were grown in germination medium (1× Murashige and Skoog (MS) salts, 1× micro-salts with Gamborg's B5 vitamins (B5), 2% sucrose, 2 g/liter gelrite, pH 5.8) for one week. The resulting hypocotyls were harvested and sliced longitudinally; the pieces were cultured on callus induction medium (1× MS salts, 1×MS vitamins, 1 mg/liter 2,4-dichlorophenoxyacetic acid (2,4D), 3% sucrose, 2 g/liter gelrite, pH 5.8) for 7 days.

The hypocotyls were bombarded with dry gold particle/DNA suspensions as described in Example 2 using 1300 psi rupture disks; the bombarded tissues were returned to callus induction medium for 3 days and then transferred to callus induction medium containing 10 mg/ml of G418. They were kept on this medium with sub-culturing every 1-2 weeks for 4-6 weeks. The subcultures were then visually analyzed for expression of the fluorescent protein as described in Example 3.

Cultures positive for expression of the fluorescent protein were further subcultured on callus induction medium containing 10 mg/ml of G418 for 4-6 weeks. During this time, fluorescent tissue was selectively isolated from non-fluorescent tissue by manipulation. Subsequently, the positive tissues were transferred to organogenesis induction media (MS salts, B5 vitamins, 6-benzylaminopurine, zeatin, sucrose, g/l gelrite, pH 5.8) containing 10 mg/ml of G418) and were kept on this medium until shoots appeared. The shoots were grown in hormone-free media to promote normal shoot development.

Developing green shoots with a defined morphology were excised and incubated in shoot elongation medium, differing from organogenesis medium by having lower cytokinin concentrations. Most callus was removed from the developing shoots, which were subcultured in fresh shoot elongation medium every 2-3 weeks. As the developing shoots became normal and exhibited apical dominance, they were transferred to rooting medium containing indolebutyric acid; the remaining callus was removed also at this time. The shoots were arranged to stand in the medium with an exposed apex. The roots began to appear in 1-3 weeks.

The rooted shoots were transferred to soil in which the basal portion of the plant was planted to soil to grow out. The shoot were gently removed from the agar and large chunks of agar were removed by rinsing gently in tap water. The roots were placed in wet RediEarth or other suitable growth medium. Roots were covered with the growth medium and packed gently. The shoots were hardened-off and acclimated to growing in soil by covering the shoot with a clear container. The shoots were placed into a greenhouse or plant growth room. After being covered for 3-4 days, the shoots were gradually exposed to room air by partial removal of the cover. Once the plant stopped wilting, the cover was removed entirely.

Several adchromosomal events and approximately 30 adchromosomal plants were obtained by this protocol; these are further discussed in example 12 and table 45. To visually analyze the presence of the marker gene in Brassica cells or tissue, a piece of leaf or other plant part was removed from a modified and control (non-modified) Brassica plant. The leaf or plant part was then examined with a fluorescence stereo-microscope using 20-100× magnification and a rhodamine filter set.

Example 7 Tomato Centromere Discovery and Mini-Chromosome Construction BAC Library Construction

A Bacterial Artificial Chromosome (BAC) library was constructed from Tomato genomic DNA isolated from Tomato variety “Microtom” and digested with the restriction enzyme MboI. This enzyme was chosen because it is methylation insensitive and therefore can be used to enrich BAC libraries for centromere DNA sequences.

Probe Identification and Selection

Tomato repetitive genomic or plastid sequences, including specific centromere-localized sequences, were initially compiled as candidate probes for hybridization with the BAC libraries. These probes represented various classes of Tomato repetitive sequences including satellite repeats (heterochromatic/centromere-specific), rDNA, and hypermethylated and highly repetitive DNA fractions.

Six probes were picked to interrogate the BAC libraries. These probes represent different groups of commonly found repetitive sequences in the Tomato genome. The probes selected are shown in Table 24 and were LESAT (the Tomato centromere satellite, in two different variants; SEQ ID NOS: 37 and 38), a tomato microsatellite (LEGATAREP; SEQ ID NO: 39), HpaII (bulk methylated DNA purified from genomic DNA by failure to digest with the methylation-sensitive enzyme HpaII), bulk repetitive DNA purified from genomic DNA by reassociation kinetics (Cot), and telomere. The probes were prepared by PCR, from cloned fragments, or from bulk methylated or repetitive DNA prepared from Tomato genomic DNA. The telomere probe sequence (SEQ ID NO: 40) was generated by PCR using the following primers: CHHZ-97 (AGGCGCGCCACCTGCAGGA GAGCTCGGTCTCA TCGAGACAC; SEQ ID NO: 41) and CHHZ-98 (GGTCGACGGCCCGGGCGTT TAAACCCGGGCTCAC; SEQ ID NO: 42). Probes were prepared and labeled with standard molecular biology methods.

TABLE 24 Tomato Repetitive Sequences and BAC Library Probes group clone used for GenBank group # name probe name Description hyb accession* 1 centromere TC2 LESAT, tomato 5012-5-11-C02 X87233.1 repeat (SEQ ID NO: 37) centromere satellite (different variant) TE1 LESAT, tomato 5012-5-11-E01 X87233.1 (SEQ ID NO: 38) centromere satellite (different variant) 2 microsatellite TE12 LEGATAREP, 5012-5-11-E12 X90937.1 repeat (SEQ ID NO: 39) tomato microsatellite repeat 3 bulk TCot6 Purified repetitive N/A N/A repetitive DNA fraction DNA T HpaII Purified N/A N/A methylated DNA fraction 4 telomere TTel Telomere PCR product N/A (SEQ ID NO: 40) *Accession number of BLAST hit; actual sequence has not been deposited in Genbank Library Interrogation and Data Analysis

The BAC clones from the libraries were spotted onto filters and these filters were hybridized with each of the probes to identify specific BAC clones that contain DNA from the group of sequences represented by the probe(s).

A total of 18,432 BAC clones from the library were interrogated with each of the probes described above sing the following hybridization conditions: 0.5×SSC 0.25% SDS at 65 degrees for 15 minutes, followed by a wash at 65 degrees for a half hour. The hybridization intensities of the BAC clones with each probe were scanned to quantitate hybridization intensity for each clone. The outputs (scores of 1 to 10 based on the hybridization intensities, with 10 being the highest intensity) were imported into a relational database, for further analysis and classification. The database contained a total of five tables that were used for BAC selection. Each table contains a total of 18,432 entries: the hybridization scores of each BAC clone from the library to one of the probes used to interrogate the library. Data analysis was done using standard SQL (Structured Query Language) routines to find BACs that contain different groups of repetitive sequences.

Classification and Selection of BAC Clones from Mini-Chromosome Construction

BAC clones containing centromeric/heterochromatic DNA were identified by their hybridization scores to different probes. The goal was to select BAC clones that contained a diverse set of various repetitive sequences. Eleven classes of centromeric BAC clones, some of which overlap, were eventually chosen to cover the broadest possible range of centromeric/heterochromatic sequences for mini-chromosome construction. Detailed descriptions of each class and probe hybridization values for each class are shown in Table 25.

TABLE 25 Classification of tomato BAC clones containing centromeric DNA Probe Hybridization Range Class LESAT LEGATA Hpa II # clones Class Properties LESAT C2 E1 REP E12 (METH) TEL identified A High N/A >=6 >=6 >=6 N/A 30 Meth, E1, E12 B High N/A >=7 N/A >=7 >=7 36 Meth, E1, TEL C High <=5 N/A N/A >=7 >=7 9 Meth, TEL; low C2 D High N/A >=8 N/A >=7 N/A 103 Meth and E1 E High N/A N/A >=6 >=6 N/A 35 Meth and E12 F High E1 N/A >=6 >=6 N/A N/A 75 and E12 G High E1 N/A >=8 N/A N/A >=8 8 and TEL H High E1 N/A >=8 <=4 <=6 N/A 89 only I High TEL N/A <=4 N/A <=4 >=8 49 only J High N/A N/A <=4 >=7 <=4 15 Meth only K High E12 N/A N/A >=7 <=4 <=4 2 only Total** 451 *Values represent hybridization intensities of an individual BAC to each probe on a scale of 1 to 10. Values were normalized N/A = not applicable

A number of representative clones from each class were chosen to yield a total of 278 BAC clones for further analysis by restriction digest fingerprinting. The BAC clones were fingerprinted (Table 26) based on restriction sites found in the centromere specific sequence(s) as described in Example 1. The restriction enzyme HinfI was used to digest the BAC clones. After fingerprinting, 100 BACs were selected for further testing using the method described in Example 1.

L. esculentum (tomato) BAC TB99 was deposited with the American Type Culture Collection (ATCC) P.O. Box 1549 Manassas, Va. 20108, USA on Feb. 23, 2005 and assigned Accession No. PTA-6603.

Thirty BAC clones (from the original 278) were selected for mini-chromosome construction based on the fingerprint class which was defined as a simple or complex laddering pattern. Table 26 lists the fingerprint patterns for a selected set of 26 Tomato BAC clones. Tomato fingerprints were classified into 3 classes: 1. high complexity (multiple large bands with no indication of laddering), 2. low ladder (predominant bands at multiples of the unit repeat size for the centromere satellite, and 3. complex ladder (features of both previous types). Table 27 lists the fingerprint classes for 7 selected tomato BACs. The preferred BACS have an *. Table 27 lists the fingerprint classes for 11 selected Brassica BACs.

TABLE 26 Restriction Endonuclease Fingerprinting of 26 Tomato BACs BAC BAC Fingerprint Number Class Class Properties Class* MiniC tested TB1 G Hi LE SAT/Tel 2. Low ladder TB1R4-3 TB4* G Hi LE SAT/Tel 2. Low ladder TB4R1-2 TB6 J Hi Hpa only 1. complex TB6R4-1 TB10 I Hi Tel only 1. complex TB10R4-1 TB12 I Hi Tel only 1. complex TB12R1-1 TB16 F Hi LESAT/LE Gata rep 2. Low ladder TB16R4-5 TB17 J Hi Hpa only 1. complex TB17R1-1 TB21 D Hi Hpa/LESAT 2. Low ladder TB21R1-2 TB22 D Hi Hpa/LESAT 2. Low ladder TB22R1-1 TB23* G Hi LESAT/Tel 2. Low ladder TB23R1-5 TB29 J Hi Hpa only 3. TB29R1-1 complex/ladder TB47 D Hi Hpa/LESAT 2. Low ladder TB47R1-1 TB55 B Hi LESAT/Hpa/TEL 2. Low ladder TB55R1-5 TB56 D Hi Hpa/LESAT 3. TB56R1-3 complex/ladder TB67 H Hi LESAT only 2. Low ladder TB67R1-1 TB72 H Hi LESAT only 3. TB72R1-3 complex/ladder TB73 D Hi Hpa/LESAT 2. Low ladder TB73R1-2 TB80* D Hi Hpa/LESAT 3. TB80R1-2 complex/ladder TB82* H Hi LESAT only 2. Low ladder TB82R1-4 TB91 H Hi LESAT only 2. Low ladder TB91R1-2 TB92 H Hi LESAT only 3. TB92R1-3 complex/ladder TB99* H Hi LESAT only 2. Low ladder TB99R1-5 TB101* B Hi LESAT/Hpa/TEL 2. Low ladder TB101R1-5 TB114 H Hi LESAT only 2. Low ladder TB114R1-1 TB115 H Hi LESAT only 2. Low ladder TB115R4-2 TB132* F Hi LESAT/LE Gata rep 2. Low ladder TB132R1-3

TABLE 27 Restriction endonuclease fingerprint classification for 7 selected tomato BACs BAC Hyb Number Class Class Properties Fingerprint Class TB4 G Hi LE SAT/Tel 2. Low ladder TB23 G Hi LESAT/Tel 2. Low ladder TB80 D Hi Hpa/LESAT 3. complex/ladder TB82 H Hi LESAT only 2. Low ladder TB99 H Hi LESAT only 2. Low ladder TB101 B Hi LESAT/Hpa/TEL 2. Low ladder TB132 F Hi LESAT/LE Gata 2. Low ladder rep Construction of Mini-Chromosomes

For each BAC identified above, a mini-chromosome was constructed using a Cre-Lox Recombination-Donor vectors as described in Example 2. Tomato mini-chromosomes were constructed from a total of 30 BACs using donor vector 151 and 153 in this assembly process, and were subsequently tested in several different tomato cell lines. Mini-chromosome genetic elements within the pCHR151 and pCHR153 vector are set out in Tables 10 and 28.

TABLE 28 Donor Components of pCHR153 Size (base Location Genetic Element pair) (bp) Details EF1α A3 2051  361-2411 Arabidopsis thaliana elongation Promoter factor 1 alpha A3 promoter (At1g07940) DsRed2 + NLS 780 2448-3227 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Pyruvate kinase 332 3362-3693 Arabidopsis thaliana pyruvate terminator kinase terminator (At5g52920) Bacterial 817 3838-4654 Bacterial kanamycin selectable Kanamycin marker Act2 terminator 800 4836-5635 Arabidopsis thaliana Actin 2 terminator MerA 1695 5789-7483 Plant selectable marker providing resistance to mercuric ions (Rugh et. al. PNAS 1996 93: 3182) Act2 1482 7486-8967 The Arabidopsis thaliana promoter + promoter Actin 2 plus natural intron intron LoxP 34 312-345 & Recombination site for Cre 8984-9017 mediated recombination (Arenski et. al 1983, Abremski et. al 1984)

Example 8

Testing of Tomato Mini-Chromosomes and Regeneration of Tomato Plants Modified with Mini-Chromosome DNA

The biolistic delivery method using wet gold particles, described in Example 2, was used to deliver mini-chromosomes to tomato cells. Functional testing of mini-chromosomes using transient assays as described in Example 3. In the transient assay, mini-chromosomes were delivered to tomato cells of a population that is undergoing cell division, in this case tomato suspension cells grown in liquid culture or callus cells grown on plates. PC703, a publicly available tomato callus cell line, was routinely used in transient assays described above. However, any actively dividing cell type can be used for this assay, such as root tissue, meristem tissue, or callus derived from any plant tissue.

After DNA delivery, the cell population was then monitored for fluorescent protein expression over the course of one to several weeks. Mini-chromosomes containing active centromeres allowed the formation of fluorescent cell clusters, which are derived from a single progenitor cell that has divided and passed the mini-c to its daughter cells. Accordingly, single fluorescent cells and clusters of fluorescent cells of various sizes were scored in the growing cell population after DNA delivery. A number of stable cell lines were obtained following the delivery of the mini-chromosomes listed in Table 29.

TABLE 29 Preferred Chromatin tomato BACs, centromeres (CEN), and mini- chromosomes (MC) based upon transient expression assays and generation of stable tomato cell lines. Stable BAC CEN MC clones Number Number Number BAC Class generated TB4 TB4 TB4R1-2 Hi LE SAT/Tel yes TB23 TB23 TB23R1-5 Hi LESAT/Tel yes TB80 TB80 TB80R1-2 Hi Hpa/LESAT yes TB82 TB82 TB82R1-4 Hi LESAT only yes TB99 TB99 TB99R1-5 Hi LESAT only yes TB101 TB101 TB101R1-5 Hi yes LESAT/Hpa/TEL TB132 TB132 TB132R1-3 Hi LESAT/LE yes Gata rep

To obtain trans-chromosomal tomato plants, the promising centromeres identified above were combined with a different set of genes than those present in donor vector 151 or 153 which were used in the construction of the initial set of 26 mini-chromosomes. The mini-chromosome construction procedure was thus repeated for BACs TB99 and TB132 using donor vectors 487-489 (See Example 2 and Tables 12-14 for description) and 531 (see Table 30 below for descriptions of the 531 donor vector), following the same steps as described above. Five mini-chromosomes were obtained that contain nptII, summarized below:

TABLE 30 Donor Components of pCHR531 Size (base Location Genetic Element pair) (bp) Details UBQ10 359  361-2398 Arabidopsis thaliana promoter polyubiquitin promoter (At4g05320) DsRed2 + NLS 780 2435-3214 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Pyruvate kinase 332 3349-3680 Arabidopsis thaliana pyruvate terminator kinase terminator (At5g52920) Bacterial 817 3825-4641 Bacterial kanamycin selectable Kanamycin marker Act2 terminator 800 4823-5622 Arabidopsis thaliana Actin 2 terminator NptII 795 5685-6479 Neomycin phosphotransferase II plant selectable marker UBQ10 intron 359 6507-6865 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression levels Pgd Fly 2140 6873-9012 PCR amplified promoter of promoter phosphogluconate dehydrogenase gene from Drosophila melanogaster LoxP 312-345 & Recombination site for Cre 9029-9062 mediated recombination (Arenski et. al 1983, Abremski et. al 1984)

Promoter driving Mini-C Cen name Cen size Donor vector nptII* TB99R7-1 TB99 50 kb pCHR487 Tef2 TB99R8-1 TB99 15 kb pCHR488 GPD-1 TB99R10-1 TB99 48 kb pCHR531 Pgd-1 TB132R8-1 TB132 48 kb pCHR488 GPD-1 TB132R10-2 TB132 27 kb pCHR531 Pgd-1

For tomato modification with these mini-chromosomes (derived from TB99 and TB132 combined with donor vectors 487, 488 and 531), the following procedure was developed. Tomato seeds were surface sterilized in 10% bleach for 15 minutes and washed 4 times with sterile distilled water. The seeds were placed in sterile Petri dishes and dried under sterile air flow in a tissue culture hood. The seeds were germinated in magenta containers on solid medium (0.5×MS salts, 1×MS vitamins, 10 g/l sucrose, 8 g/l tissue culture agar, 0.5 mM MES, 1.3 g/liter calcium gluconate, pH 5.8) for 8 days at ambient temperature under lights.

Cotyledons and hypocotyls were removed from the seedlings for explants. The cotyledon pieces were cut into slices approximately 3-4 mm wide and the hypocotyls were cut longitudinally. Both types of explants were grown on preculture medium (1× MS salts, 1×MS vitamins, 3% sucrose, 1 mM MES, 8 g/liter tissue culture agar; pH 5.7-5.8) The medium also contained either 1 mg/l BA+0.1 mg/l non-essential amino acids or 0.75 mg/1 zeatin+1 mg/l IAA. The cotyledon pieces were cultured with the abaxial side in contact with the medium; while the hypocotyls pieces were cultured with the wounded side away from the medium. The explants were pre-cultured for 3-6 days under lights.

The explants were then transferred to 5 cm polyethylene mesh circles and bombarded using the wet biolistics method as described in Example 2. The same surface was bombarded as facing upwards (away from the medium) during pre-culturing. After bombardment, the explants were transferred back onto preculture medium and kept under light.

Two days after bombardment, the explants were transferred onto preculture medium containing 100 mg/liter kanamycin. The explants were cultured on this medium under light for 6 weeks to three months with sub-culturing onto fresh medium every 3 weeks. Starting at 6 weeks after the onset of selection, the explants were screened with a fluorescence stereomicroscope for appearance of fluorescent calli or shoots.

The presence of fluorescent protein expression was detected as described in Example 3. Fluorescent calli or shoots were removed from the explants and transferred to plates with MS3 basal medium (1× MS salts, 1× Gamborg's vitamins, 3% sucrose, 0.5 mM MES, 8 g/liter tissue culture agar, pH 5.8)+0.75 mg/l zeatin. The calli were grown on this medium until visible shoots formed. The shoots arising directly from the kanamycin plates were kept on this medium for only 1-2 weeks. The shoots were then transferred to MS3 basal medium+0.1 mg/liter zeatin and were subcultured on this medium until the shoots elongated (1-3 cm shoot length, at least 5 mm of stem length), with medium changes every 2 weeks.

The elongated shoots were transferred to magenta containers containing 0.5×MS salts, 1×MS vitamins, 1% sucrose, 0.1 mg/liter IBA, 1 mM MES, pH 5.7-5.8. Rooting was allowed to proceed until well-formed roots generated (2 weeks to 2 months). Plantlets were then transferred to soil.

Table 31 lists the number of trans-chromosomal events for tomato and tobacco.

TABLE 31 Construct # events Tobacco transformants with tomato mini-C's - summary of events TB99R7-1  9 TB99R10-1  3 TB132R10-2  2 TB99R8-1  1 TB132R8-1  2 Tomato transformants with tomato mini-C's - summary of events TB99R7-1  13* TB132R10-2  10* *not all events fully regenerated, some of them still in organogenic phase

Example 9 Regeneration of Tobacco Plants Modified with Mini-chromosome DNA

The biolistic delivery method using wet gold particles, described in Example 2, was used to deliver tomato mini-chromosomes (described in Example 7) to Tobacco cells.

An explant from a tobacco leaf was cut using a cork borer. The leaves were immersed in MS medium during cutting to avoid tissue dehydration. The leaf disks were placed adaxial side up onto plates containing callus inducing medium with vitamins (4.44 g/L MS Basal Medium w/Gamborg Vitamins, 0.5 g/L MES, 3% sucrose, 0.5% tissue culture agar, non-essential amino acids, kinetin and 4 ml of 1000× Gamborg Vitamins, pH 5.8). After four days, the explants were bombarded with wet gold particles/DNA suspension as described in Example 2 using 450 psi rupture disks with the sample tray in the lowest position. For bombardment, explants were transferred onto 50 mm polyethylene mesh circles, and covered with mosquito netting.

Immediately after bombardment, all explants were returned to their original plates for 24 hours. Subsequently, the explants were transferred to MBNV plates (4.44 g/L MS Basal Medium w/Gamborg Vitamins, 0.5 g/L MES, 3% sucrose, 0.5% tissue culture agar, 0:1 mg/L NAA, 2.0 mg/L BA, 4 ml of 1000× Gamborg Vitamins pH 5.8) containing 50 μg/ml of kanamycin. After 5 days of selection, the explants were transferred to fresh MBNV plates containing 100 μg/ml kanamycin for 10 days. Subsequently, the explants were transferred to MBN plates (MBNV plates described above but without the added vitamins; 1× final concentration of Gamborg's vitamins), containing 100 μg/ml of kanamycin. These plates were subsequently subcultured about every 2 weeks afterwards, onto the same MBN plates containing 100 μg/ml of kanamycin.

The presence of fluorescent protein expression was detected as described in Example 3. A pea-sized fluorescent calli was removed from the plate and transferred to MBN medium without kanamycin. Fluorescent shoots were removed from the callus as they developed, and these shoots were transferred to Magenta containers containing 1×MS salts, 1×MS vitamins and 2% sucrose, pH 5.8. As the shoots enlarged and root formed, they were transferred to Magenta containers containing 0.5×MS salts, 0.5×MS vitamins and 1% sucrose. The transchromosomal events for tobacco plants are described above in Table 31.

Example 10 Soybean Centromere Discovery and Mini-Chromosome Assembly and Construction

BAC Library Construction

A Bacterial Artificial Chromosome (BAC) library was constructed from Soybean genomic DNA isolated from Glycine max variety “Williams 82” and digested with the restriction enzyme MboI This enzyme was chosen because it is methylation insensitive and therefore can be used to enrich BAC libraries for centromere DNA sequences.

Probe Identification and Selection

Five groups of soybean repetitive genomic or plastid sequences, including specific centromere-localized sequences, were initially compiled as candidate probes for hybridization with the BAC libraries (Table 32). These probes represented various classes of Soybean repetitive sequences including satellite repeats (heterochromatic/centromere-specific), retroelements, telomeres, rDNA, and hypermethylated DNA fractions.

Seven probes were picked to interrogate the BAC libraries. These probes represent different groups of commonly found repetitive sequences in the Soybean genome. The probes selected are shown in Table 32 and were: two variants of the soybean centromere satellite (TRS and 3×1), 5S ribosomal DNA, plant telomeres, HpaII (bulk methylated DNA purified from genomic DNA by failure to digest with the methylation-sensitive enzyme HpaII) and Sau3A (bulk methylated DNA purified from genomic DNA by failure to digest with the methylation-sensitive enzyme Sau3A), and retroelement. The probes were prepared from cloned fragments isolated or from bulk methylated DNA prepared from Soybean genomic DNA. Sequences from the or PCR primes clones used to prepare each probe are shown in Table 32. The telomere probe sequence (SEQ ID NO: 40) was generated by PCR using the following primers: CHHZ-97 (AGGCGCGCCACCTGCAGGAGAGCTCGGTCTCA TCGAGACAC; SEQ ID NO: 41) and CHHZ-98 (GGTCGACGGCCCGGGCGTT TAAACCCGGGCTCAC; SEQ ID NO: 42). Probes were prepared and labeled with standard molecular biology methods.

TABLE 32 Soybean Genetic Repetitive Sequences and BAC Library Probes Group Group # Name Probe Name Description Clone used for hyb GenBank accession* 1 Cen repeat SC2 TRS (centromere satellite 5012-5-9-C02 gi|11464861|gb|AF297984.1|AF297984 (SEQ ID NO: 43) repeat variant) Glycine max clone TRS2 gi|11464862|gb|AF297985.1|AF297985 Glycine max clone TRS3 gi|11464860|gb|AF297983.1|AF297983 Glycine max clone TRS1 (SEQ ID NO: X) SE7 3X1(centromere satellite 5012-5-9-E07 Z26334.1|GMP3X1SAT (SEQ ID NO: 44) repeat variant) (SEQ ID NO: X) 2 rDNA SC11 5S rDNA 5012-5-9-C11T X06044.1|GMRN45SI Soybean (SEQ ID NO: 45) 4.5 - 5S rRNA intergenic (SEQ ID NO: X) 3 retroelement SG12 retrovirus-like element 5012-5-9-G12T AF186186 (SEQ ID NO: 46) (SEQ ID NO: X) 4 bulk SHpaII Purified methylated DNA N/A N/A repetitive fraction DNA SSau Purified methylated DNA N/A N/A fraction 5 telomere Stel Telomere PCR product N/A (SEQ ID NO: 40) *Accession number of BLAST hit; actual sequence has not been deposited in Genbank Library Interrogation and Data Analysis

The BAC clones from the libraries were spotted onto filters and these filters were hybridized with each of the probes to identify specific BAC clones that contain DNA from the group of sequences represented by the probe(s).

A total of 18,432 BAC clones from the library were interrogated with each of the probes described above sing the following hybridization conditions: 0.5×SSC 0.25% SDS at 65 degrees for 15 minutes, followed by a wash at 65 degrees for a half hour. The hybridization intensities of the BAC clones with each probe were scanned to quantitate hybridization intensity for each clone. The outputs (scores of 1 to 10 based on the hybridization intensities, with 10 being the strongest intensity) were imported into a relational database, for further analysis and classification. The database contained a total of seven tables. Each table contains at total of 18,432 entries: the hybridization scores of each BAC clone from the library to one of the probes used to interrogate the library. Data analysis was done using standard SQL (Structured Query Language) routines to find BACs that contain different groups of repetitive sequences.

Classification and Selection of BAC Clones for Mini-Chromosome Construction

BAC clones containing centromeric/heterochromatic DNA were identified by their hybridization scores to different probes. The goal was to select BAC clones that contained a diverse set of various repetitive sequences. Twelve classes of centromeric BAC clones, some of which overlap, were eventually chosen to cover the broadest possible range of centromeric/heterochromatic sequences for mini-chromosome construction. Detailed descriptions of each class and probe hybridization values for each class are shown in Table 33.

TABLE 33 Classification of Soybean BAC clones containing centromeric DNA Probe Hybridization Range 5S Class TRS 3X1 rDNA RE Meth Meth # clones Class Properties (C2) (E7) (C11) (G12) (HpaII) (Sau3A) TEL identified A High 3X1 <=4 >=10  N/A N/A >=1 N/A N/A 155 B High TRS >=10  <=4 N/A N/A >=1 N/A N/A 114 C High <=10  <=10  N/A N/A >=7 N/A N/A 43 HpaII D High <=4 <=4 N/A N/A >=5 N/A N/A 44 HpaII only E High TRS >=6 N/A N/A N/A >=5 N/A N/A 34 and HpaII F Highest N/A >=6 N/A N/A >=5 N/A N/A 103 3X1 and High HpaII G High 3X1 N/A >=6 N/A N/A >=5 N/A N/A 103 and Highest HpaII H High TRS >=8 >=8 N/A N/A >=1 N/A N/A 54 and 3X1 I High >=7 >=7 N/A N/A >=4 N/A N/A 5 TRS, 3X1, HpaII J High >=6 >=6 N/A N/A >=4 N/A N/A 33 TRS, 3X1, HpaII K High TEL >=1 >=1 N/A N/A >=1 N/A >=8 6 L High RE >=1 >=1 N/A >=8 >=1 N/A N/A 105 Total** 642 N/A = not applicable; This is functionally equivalent to >=1, as well as <=10 Classes F and G have the same threshold values but the selected clones for class F show the highest 3X1 scores of all the clones in the class; For class G, the selected clones show the highest HpaII scores for the class., and Classes I and J have the same criteria, but slightly different thresholds.

A number of representative clones from each class were chosen to yield a total of 230 BAC clones for further analysis by restriction digest fingerprinting. The BAC clones were fingerprinted (Table 34) based on restriction sites found in the centromere specific sequence(s) as described in Example 1. The restriction enzymes HinfI and DdeI were used to digest the BAC clones. After fingerprinting, 33 BACs were selected for further testing using the method described in Example 1.

Thirty-three BAC clones (from the original 230) were selected for mini-chromosome construction and testing based on the fingerprint class which was defined as a simple or complex laddering pattern. Soybean fingerprints were classified into 3 classes: 1. high complexity (multiple large bands with no indication of laddering), 2. low ladder (predominant bands at multiples of the unit repeat size for the centromere satellite, and 3. complex ladder (features of both previous types). Table 34 lists the fingerprint patterns for this selected set of Soybean mini-chromosomes. The preferred BACs have an *. Table 35 lists the fingerprint classes for 10 selected soybean BACs.

TABLE 34 Restriction endonuclease fingerprinting of 33 soybean BACs HinfI DdeI BAC BAC Class Fingerprint Fingerprint Number Class Properties Class Class MiniC tested SB1 J High TRS, n/d* 4. 6 bands/9 SB1R3-1 3X1, HpaII bands SB2 D High HpaII 4. 6 bands/ 4. 6 bands/9 SB2R5-1 only 9 bands bands SB3* H High TRS 3. complex 3. complex SB3R1-1 and 3X1 ladder ladder SB6* B High TRS 2. simple 2. simple SB6R15-3 ladder ladder SB8 A High 3X1 1. complex 1. complex SB8R3-1 SB9* H High TRS 3. complex 2. simple SB9R8-1 and 3X1 ladder ladder SB10 L High RE 1. complex 1. complex SB10R4-1 SB11* B High TRS 3. complex 3. complex SB11R3-1 ladder ladder SB11R3-2 SB11R3-3 SB12* B High TRS 3. complex n/d* SB12R2-1 ladder SB12R2-2 SB12R2-3 SB21 K High TEL 2. simple 1. complex SB21R1-2 ladder SB22* A/L High 2. simple 1. complex SB22R2-1 3X1/RE ladder SB24 A/L High 2. simple 1. complex SB24R2-3 3X1/RE ladder SB29 B High TRS n/d* 3. complex SB29R2-2 ladder SB38* H High TRS n/d* 3. complex SB38R2-1 and 3X1 ladder SB38R2-2 SB41 H High TRS n/d* 2. simple SB41R3-1 and 3X1 ladder SB45 J High TRS, 4. 6 bands/ 4. 6 bands/ SB45R5-1 3X1, HpaII 9 bands 9 bands SB50* B High TRS 3. Complex n/d* SB50R1-1 ladder SB62 A High 3X1 2. Simple n/d* SB62R1-2 ladder SB93 B High TRS 3. complex n/d* SB93R3-2 ladder SB93R3-3 SB97 A High 3X1 2. simple n/d* SB97R3-2 ladder SB102 A High 3X1 2. simple n/d* SB102R3-1 ladder SB107 B High TRS 2. simple n/d* SB107R3-1 ladder SB111 A High 3X1 2. simple n/d* SB111R3-1 ladder SB112 A High 3X1 3. complex n/d* SB112R3-1 ladder SB116* A High 3X1 2. simple n/d* SB116R3-1 ladder SB118 A High 3X1 2. simple n/d* SB118R3-1 ladder SB119 A High 3X1 2. simple n/d* SB119R3-2 ladder SB123 A High 3X1 2. simple n/d* SB123R3-2 ladder SB125* B High TRS 3. complex n/d* SB125R3-1 ladder SB135 B High TRS 2. simple n/d* SB135R3-2 ladder SB138 A High 3X1 2. simple n/d* SB138R3-1 ladder SB178 B High TRS 2. simple n/d* SB178R3-1 ladder SB219 B High TRS 2. simple n/d* SB219R3-3 ladder

TABLE 35 Restriction endonuclease fingerprint classification for 10 selected soybean BACs BAC Class Fingerprint Class Number Class Properties HinfI DdeI SB3 H High TRS and 3. complex 3. complex 3X1 ladder ladder SB6 B High TRS 2. simple ladder 2. simple ladder SB9 H High TRS and 3. complex 2. simple ladder 3X1 ladder SB11 B High TRS 3. complex 3. complex ladder ladder SB12 B High TRS 3. complex n/d* ladder SB22 A/L High 3X1/RE 2. simple ladder 1. complex SB38 H High TRS and n/d* 3. complex 3X1 ladder SB50 B High TRS 3. Complex n/d* ladder SB116 A High 3X1 2. simple ladder n/d* SB125 B High TRS 3. complex n/d* ladder

G. Max (soybean) BAC SB6 was deposited with the American Type Culture Collection (ATCC) on P.O. Box 1549 Manassas, Va. 20108, USA on Feb. 23, 2005 and was assigned Accession No. PTA-6602.

Construction of Mini-Chromosome

Each of the soybean BAC clones identified above were constructed using a Cre-Lox Recombination-Donor as described in Example 2. Soybean mini-chromosomes were constructed from a total of 33 BACs using donor vector pCHR151 in this assembly process, and were subsequently tested in several different soybean cell lines. Mini-chromosome genetic elements within the pCHR151 are described above in Table 10. The Soybean mini-chromosomes were used to transform broccoli plants (see Table 37 below).

Identification of Functional Soybean Centromeres

Functional testing of mini-chromosomes using transient assays as described may be carried out as in Example 3. Mini-chromosomes are delivered to the soybean cells using wet biolistic as described in Example 2. After DNA delivery, the cell population is then monitored for fluorescent protein expression over the course of one to several weeks. Mini-chromosomes containing active centromeres will allow the formation of fluorescent cell clusters, which are derived from a single progenitor cell that has divided and inherited the mini-chromosome to its daughter cells. Accordingly, single fluorescent cells and clusters of fluorescent cells of various sizes are scored in the growing cell population after DNA delivery. Standard protocols for soybean tissue culture and transformation, including those available at the University of Iowa, School of Agriculture web site, are used to regenerate adchromosomal soybean plants.

Mini-Chromosome Autonomy.

As a direct demonstration of mini-chromosome autonomy, circular constructs were recovered from fluorescent soybean cell lines that had been propagated for 5 months (˜25 generations) following bombardment. Genomic DNA was extracted from a cell line containing SB12MC, and the DNA was treated with a highly processive exonuclease, resulting in degradation of all linear DNA fragments including those derived from host chromosomes. Surviving DNA molecules were introduced into E. coli and transformants were selected on antibiotic-containing medium.

Genomic DNA from unmodified soybean cells did not result in any antibiotic-resistant colonies, while DNA purified from the line containing mini-chromosomes yielded 13 independent modified colonies (2 from exonuclease-treated DNA and 11 from untreated DNA, R1-R13). DNA was extracted from each transformed E. coli clone and characterized by gel electrophoresis and sequencing. While the vector backbone of the rescued mini-chromosomes was typically unchanged (9/13 transformants). BAC-end sequencing demonstrated that 11/13 of the recovered clones retained the same DNA sequence junctions at the centromere cloning boundaries as the parental molecule (600/600 bp sequenced at each junction), including two of the mini-chromosomes with altered vector sequences.

Fluorescence in situ hybridization (FISH) was carried out to examine mini-chromosome autonomy and copy number. Cells containing mini-chromosomes were arrested in metaphase, spread on slides and probed with labeled soybean centromere satellite DNA (red) and mini-chromosome vector sequences. In cells hybridizing to both the centromere and vector probes, only one autonomous mini-chromosome was identified; similar signals were not detected in non-transgenic controls. Only a subset of the native centromeres were labeled, suggesting that the satellite sequence used as a probe is chromosome-specific. Strong vector hybridization signals were not detected within the host chromosomes, providing further evidence that the mini-chromosome DNA remained autonomous.

Satellite Sequences from Mini-Chromosomes

The identified soybean mini-chromosomes defined DNA sequences sufficient for centromere activity. The sequence content of the centromere-containing BAC clones and the mini-chromosomes derived from them with quantitative dot blots, using probes that correspond to i) vector sequences, ii) soybean satellites, iii) the SIRE retroelement, and iv) 28S rDNA, all of which are highly repetitive sequences present in the soybean centromeric region. BAC SB1 lacked centromere activity and has a high rDNA content with undetectable satellite and retroelement sequences. By contrast, the mini-chromosome derivatives of SB6 and SB12 had similar compositions, with 6.4 and 11.8 kb of centromere satellite, respectively. The recovered SB12 derivatives retained the parental composition (R4, R6, R7, R10), had a two-fold decrease in satellite (R1, R2, R3, R5), or had little or no satellite (R8, R9, R11, R12, R13). The SIRE retroelements present in SB12 were retained in most of the derivatives, suggesting little selective pressure to eliminate this sequence during growth of the modified cell culture. In addition, each mini-chromosome also contained ˜8.5 kb of gene sequence from pCHR151 (Table 10).

DNA sequencing of SB12R2-3 (1.4-fold insert coverage) revealed ˜80% of the insert was composed of tandem satellite repeats (Genbank U11026 and Z26334), ˜9.9% was made up of retroelement-related sequences, and ˜10.1% represented novel, contiguous sequence. The same analysis also produced 1.6-fold vector sequence coverage, indicating little if any cloning bias against fragments from the centromere. Individual satellite repeats showed an average of 91.3% (s.d.=11.3%) identity to each other, with specific regions showing significantly higher and lower levels of variability. Comparing the satellite repeat consensus from SB12R2-3 to that obtained from random satellite sequences (CrGm1 and CrGm2) identified several bases that differed significantly (χ² test, P<0.05). The SB12R2-3 satellite repeats showed an average length of 91.07±0.40 bp, similar to the CrGm2 91-base consensus and differing from the CrGm1 92-base consensus. FIG. 6 shows an alignment of these consensus sequences.

Example 11 Analysis of Mini-Chromosomal DNA Expression in Transgenic Plants Visual Scoring

The adchromosomal plants described above in Example 4 (broccoli), Example 5 (canola), Example 6 (tobacco) and Example 7 (tomato) were tested to determine if the mini-chromosome DNA was being expressed. The presence of visible marker genes allowed for visual analysis to determine if the regenerated plants were expressing the fluorescent protein present on the mini-chromosome. For visual analysis, a piece of a leaf or other plant part was cut from the adchromosomal plant. A similar part is cut from a control plant (non-adchromosomal). The plants were analyzed under a fluorescence stereo-microscope as described in Example 3.

Table 37 displays the results of visual scoring of T0 adchromosomal plants.

TABLE 37 No. of Centromeres Tested Host and Origin of Centromere No. of Positives Scored In Broccoli 15 (13 broccoli, 1 soybean 12 (10 broccoli, 1 plants and 1 tobacco) soybean and 1 tobacco) Broccoli 15 (13 broccoli, 1 soybean 14 (12 broccoli, 1 cluster and 1 tobacco) soybean and formation 1 tobacco) Canola  1 (broccoli)  1 plant Canola 34 (broccoli) 10 cell culture Tobacco  2 (tomato)  2 plants Tomato  8 (tomato)  2 plants Tomato 20 (tomato)  2 cell culture

Expression of the fluorescent protein gene encoded by the mini-chromosome was readily observed in the cells of a piece of tissue such as leaf or root taken from a transchromosomal plant under a fluorescence stereo-microscope. Fluorescence was very high and uniform throughout the tissue. Sectoring of fluorescence protein expression was observed in some cases.

PCR Analysis

PCR was used to amplify sequences within the mini-chromosome. This method allowed for detection of all mini-chromosome parts or a subset of parts. PCR analysis was also carried out in DNA samples isolated from whole cell DNA preparations from adchromosomal broccoli, canola and tobacco plants. A piece of leaf was cut from the plant and ground by hand using a pestle and a microcentrifuge tube. The DNA was isolated using Qiagen Kit (catalog no. 69106) according to the manufacturer's instructions. PCR reactions were carried out as follows: 3 μl template DNA, 2.5 μl of 10× Termopol buffer (New England Bioscience, Catalog No. B9004S), 0.5 μl dNTP's (10 mM each), 1.5 μl oligo 1 (20 μM), 1.5 μl oligo 2 (20 μM), 15.5 μl dH₂O and 0.5 μl Taq polymerase (New England Bioscience, Catalog No. M0267S). The Oligos used either detected the DsRed gene (CHHZ 150 and 152) or the UBQ10 promoter (CHHZ 467 and 469). To detect DsRed oligo CHHZ 150 (TGAACGGCCACGAGTTCGAGATCG; SEQ ID NO: 47) and oligo CHHZ 150 (GTCCTCGTTGTGGGAGGTGATGTC; SEQ ID NO: 48) were used. To detect the UBQ10 promoter oligo CHHZ467 (CTGCCACTCCATTTCCTTCTCGGC; SEQ ID NO: 49) and oligo CHH469 (ACTTATCCGGTCCTAGATCATCAG; SEQ ID NO: 50) were used. The results of the PCR analysis are displayed in Table 38.

TABLE 38 No. of Plants No. of PCR No. of Visual Host No. of Events Tested Positives Positives Broccoli 74 140 127 128 Canola 6 55 35 32 Tobacco 24 61 16 20 Western Blot

Expression of the fluorescent protein DsRed in the adchromosomal broccoli plants was measured by Western blot analysis. Leaf tissue, obtained using a cork borer, was ground to a fine powder using a chilled pestle and the leaf tissue was lysed using Novex Tris-Glycine SDS Sample Buffer (2×) on ice. The protein sample concentration was determined using the BAC assay and the samples were separated on a tris-glycine gel (4-20%) according to the manufacturer's instructions (Novex). A protein sample from a non-adchromosomal broccoli plant was run as a negative control. Boiled purified E. coli purified DsRed was run as a positive control. The protein was transferred from the gel to filter paper (nitrocellulose or PVDF). The filter was immunoblotted with an anti-DsRed primary antibody (Clontech), which was detected with an HRP-labeled secondary antibody and developed with Pierce Supersignal West Pico Chemiluminescent Substrate. Table 39 summarizes the Western Blot analysis.

TABLE 39 Broccoli Centromeres in Soy Centromeres Broccoli in Broccoli No. tested No. positive No. tested No. positive Centromere 9 9 1 1 Mini- 28 28 1 1 chromosomes Events 51 47 3 3 Plants 136 119 4 4

Expression of the DsRed mRNA in the adchromosomal broccoli plants was also analyzed by RT-PCR. Total RNA was isolated from plant tissue using the Qiagen mini-kit (catalog no. 74104) according to the manufacturer's instructions. The reverse transcriptase reaction was carried out with 11 μl DNAase I-treated total RNA, 1 μl oligo-DT (oligo CHR152 specific for DsRed), 1 μldNTP (10 mM each). The reaction was heated to 62° C. for 2 minutes and chill on ice, then the following was added: 4 μl 5×1^(st) stand buffer (Invitrogen), 2 μl DTT (Invitrogen) and 1 μl Superscript II reverse transcriptase. The mixture was incubated at 42° C. for 1 hour. Subsequently, 80 μl of dH2O was added and the mixture was heat inactivated for 15 minutes at 70° C.

The cDNA samples generated by the reverse transcriptase reaction were amplified with a PCR reaction carried out with 5 μl cDNA, 2.5 μl 10× Themopol buffer (New England Bioscience), 0.5 μl dNTPs (10 mM each), 1.5 μM oligo 1 (20 μM each), 1.5 μl oligo 2 (20 mM each) 13.5 μl H2O and 0.5 μl Taq polymerase (New England Bioscience). 83 adchromosomal broccoli plants were tested and 69 were positive for DsRed mRNA expression (73 were positive by visual analysis).

Table 40 is a summary of the visual, PCR, Western, and RT-PCR data for the adchromosomal broccoli plants.

TABLE 40 West- Vis- Con- Centro- Event PCR RT ern ual struct mere # Genes # Plants 4 + + + + 5R4-1 BB5 2 8 6 + + + + 5R4-1 BB51 2 5 7 + + + + 5R4-1 BB5 2 22 10 + + + + 5R4-1 BB5 2 16 15 + + + + 5R4-1 BB5 2 10 17 + + + + 5R4-1 BB5 2 17 18 + + + + 71R1-1 BB71 2 4 23 + + + + 489 integrative 2 1 35 + + + + 816-2 BB5 4 4 39 − − − − 817-A BB5 4 13 40 + + + + 817-A BB5 4 3 51 + + + + 817-A BB5 4 7 52 + + + + 819-A BB5 4 4 53 + + + + 819-A BB5 4 3 55 + + + + 819-A BB5 4 6 67 + + + + 824-9 BB5 4 2 69 + + + + 824-9 BB5 4 5 83 − − − − 591-1L BB5 3 5 112 + − − − 593-4L BB5 3 5 119 + + + + 593-4L BB5 3 4

Example 12 Analysis of Autonomy and Integration of Mini-Chromosomes in Adchromosomal Broccoli Plants

Southern Blot

Southern blot analysis was carried out to analyze whether the mini-chromosome was autonomous or integrated into the genome of the of the adchromosomal T0 broccoli plants. An autonomous mini-chromosome will have the same restriction pattern as wild type plant DNA spiked with mini-chromosome DNA, while a mini-chromosome that has integrated into a host chromosome will have an altered restriction pattern and that altered restriction pattern is not predictable. If integration does occur and the junction between the host chromosome DN is in the centromeric region of the mini-chromosome, a restriction pattern similar to an autonomous mini-chromosome is expected. This is true because only the “gene region” (the part of the mini-chromosome excluding the centromere region) is subsequently used as a probe, as described below.

Plant tissue from the adchromosomal and control broccoli plants was ground to a fine powder in liquid nitrogen using mortar and pestle. Genomic DNA was isolated from the homogenized plant cells using phenol:chloroform:isoamyl alcohol extraction as taught by Csail et al., (Plant Mol. Biol. Rep. 16: 69-89, 1998). The DNA samples (5 μg) were digested with BglII restriction enzyme diluted in enzyme buffer, 100×BSA, 100 mM β-mercaptoethanol, 100 mM spermidine, dH₂O. The DNA was digested overnight at 37° C. Subsequently, an additional 2 μl of BglII was added to the DNA and allowed to digest a few additional hours. Loading buffer was added and the samples were separated on a 0.7% agarose gel. The DNA on the gel was visualized using ethidium bromide. The DNA on the gel was transferred to a nylon membrane using a Bio-Rad Vacuum Blotter (Model 785). The filters were probed with radiolabeled DNA complementary to the gene region of the mini-chromosome (entire sequence excluding the centromere region).

Southern blot analysis was carried out on 60 adchromosomal broccoli plants in which 32 events were tested, 7 centromeres were tested (6 broccoli centromeres and 1 soybean centromere). 40% of the samples were tested in duplicate. The Southern Blot results are summarized in Table 41. In the majority of events, the gene region of the mini-chromosome was intact and the results indicate the mini-chromosomes were autonomous or integrated via the centromere sequence. BB5R4-1

TABLE 41 No. of Mini- Events Consistent with Not chromosome Centromere Tested Autonomy Integration Detected 5R4-1 BB5 6 1 5 — 5R16-6 BB5 1 1 — — 817 BB5R4-1 2 1 — 1 818 BB5R4-1 1 1 — — 819 BB5R4-1 4 4 — — 820 BB5R4-1 1 — — 1 823 BB5R4-1 3 3 — — 824 BB5R4-1 2 1 — 1 591-1 BB5R4-1 2 1 — 1 593-3L BB5R4-1 1 1 — — 593-4L BB5R4-1 1 — 1 — 816-2 BB5R4-1 2 2 — — 965 BB15R4-1 1 1 — — 964-4 BB15R4-1 1 — — 1 967 BB16R1-2 1 1 — — 222R2-1 BB222 1 — — 1 972-5 BB60R1-1 1 1 — — SB986-1 SB38R2-2 1 1 — — Total 32 20  6 6 Fluorescence In Situ Hybridization

Fluorescence in situ hybridization (FISH) is carried out to determine the autonomy of the mini-chromosomes in root tips and anthers from the adchromosomal T0 broccoli plants. The tissues were probed with labeled pCHR151 and pCHR08, and BB5 PCRed BSAT and stained with DAPI. For analysis, the FISH chromosomal spreads needed to meet the following criteria: condensed and well-spread chromosomes, free of major background, strong centromere hybridization, 18 chromosomes, signal localized to approximately the same place on same chromosome. Integration is determined by detecting the mini-chromosome and it is associated with the genome and autonomy is determined by detecting the mini-chromosome and it was free of the genome. If the mini-chromosome is detected to be both free and associated with the genome it is both autonomous and integrated mini-chromosomes are present.

Example 13 Analysis of Mini-chromosomes in Ti Brassica Pollen and T1 Brassica Plants

To analyze the presence of the mini-chromosome in pollen isolated from a flowering adchromosomal T0 Brassica plant (T1 pollen), two anthers from each of three flowers were removed. The anthers were harvested from flowers that were open for more than a half a day and were shedding pollen. The anthers were streaked on a plate of sterile medium containing 1×MS salts, 13% sucrose, 0.8% tissue culture agar, pH 5.8, depositing a streak of pollen onto the surface of the plate. In a darkened room, the pollen was examined with a fluorescence stereo-microscope using 100× magnification and a rhodamine or FITC filter set. At least 500 pollen cells in groups of 100 were counted. Total pollen cells were counted under visible light and then examined under fluorescence.

T1 pollen was analyzed from adchromosomal T0 broccoli plants. The broccoli pollen visual data is summarized in Table 42.

TABLE 42 % of Pollen Grains Plant Event Expressing DsRed Pbo4A 4 0% pbo4E2 4 no pollen pbo7BCopy 7 0% pbo7C 7 no pollen pbo7C1Copy 7 no pollen pbo7S 7 0% pbo10C2 10 no pollen pbo10C2Copy 10 no pollen pbo10D3 10 no pollen pbo15E1 15 0% pbo15E2 15 7% pbo15M1 15 1% pbo15O 15 0% pbo17A1 17 0% pbo17C2 17 0% pbo17G1 17 0% pbo17N1 17 0% pbo18A 18 1% pbo18B 18 0% pbo19G3 19 4% pbo28A 28 0% pbo39B1 39 0% pbo39C 39 0% pbo40A 40 32%  pbo40D 40 25%  pbo51C 51 4% pbo51D 51 0% pbo52A 52 0% pbo52C 52 1% pbo53A 53 8% pbo55B 55 4% pbo69A1 69 0% pbo83A1 83 0% pbo112A3 112 no pollen pbo119A 119 no pollen pbo126A 126 0% pbo126B 126 3% pbo173D 173 no pollen pbo221A 221 14%  pbo222E 222 2%

Adchromosomal T1 broccoli plants were generated by selfing or outcrossing. All crosses were done by bud pollination to overcome self-incompatibility and/or to ensure that the donor pollen gave rise to all seeds in the pod. To perform a bud pollination, an unopened flower was stripped of all sepals, petals and stamens, leaving only the immature pistil. Pollen from the appropriate plant was applied to the stigma. The flower was labeled and the pod allowed to develop normally The presence of the mini-chromosome in the adchromosomal T1 broccoli plants were analyzed visually and by PCR as described in Example 8. Three mini-chromosomes comprising one of two centromere sequences (with 2 and 4 genes) were analyzed. The data from the adchromosomal T1 broccoli plants is summarized in Table 43 and Table 44.

TABLE 43 T1 Adchromosomal_Broccoli Plants Visual Visual Visual scoring of scoring of Scoring T1 seedlings T1 seedlings of T1 PCR on (outcross - (outcross - seedlings negative male) female) (self) seedlings Event tested positive tested positive tested positive tested positive 4 68 0 55 0 — — 57 0 17 158 0 — — 1 0 95 0 17 70 0 — — 1 0 — — 17 39 0 67 0 17  1 — — 17 9 0  4 0 — — 13 1 18 11 0 52 5 — — — — 18 34 0 — — — — — — 40 46 0  4 3 9 7  3 0

TABLE 44 T1 Adchromosomal Broccoli Plants Visual PCR of Donor Recipient Self Negatives Plant Event Tested Positive Tested Positive Tested Positive Tested Positive pbo4A 4 69 0 55 0 0 0 57 0 pbo17A1 17 258 0 51 0 9 0 98 0 pbo17A3 17 77 0 1 0 1 0 0 0 pbo17C2 17 43 0 65 0 20 0 0 0 pbo17G1 17 0 0 4 1 0 0 0 0 pbo17N1 17 9 0 4 0 10 0 13 0 pbo18A 18 248 0 52 0 6 0 0 0 pbo18B 18 50 0 29 0 0 0 0 0 pbo22 22 66 0 0 0 0 0 0 0 pbo40A 40 56 28 3 1 9 7 59 27 pbo40D 40 65 32 22 13 40 31 0 0 pbo51A 51 64 0 0 0 12 0 0 0 pbo51C 51 101 0 63 2 0 0 0 0 pbo51D 51 0 0 0 0 2 0 0 0 pbo52C 52 83 0 236 6 59 0 0 0

Pollen was also analyzed from transformed T0 canola plants (Brassica napus) by visual analysis. The visual data is summarized in Table 45.

TABLE 45 Brassica napus pollen fluorescence summary % Event # pollen fluorescent Plant # Mini-C counted pollen Flower size 11-1-2 11 pCHR820-1 568 87.5% large 11-1-4 11 pCHR820-1 558 88.9% large 11-2 11 pCHR820-1 637 68.8% N.R. 11-3-1-1 11 pCHR820-1 613 52.7% small 11-3-1-2 11 pCHR820-1 667 63.7% small 11-6-1 11 pCHR820-1 591 98.0% large 11-6-2 11 pCHR820-1 580 96.6% large 11-6-3 11 pCHR820-1 640 93.8% large 11-6-4 11 pCHR820-1 585 95.2% large 11-7 11 pCHR820-1 607 67.2% small 11-8-1-1 11 pCHR820-1 540 65.4% N.R. 11-8-1-2 11 pCHR820-1 584 62.5% small 11-8-1-3 11 pCHR820-1 512 64.8% N.R. 11-8-2 11 pCHR820-1 542 66.4% N.R. 11-8-2-2 11 pCHR820-1 652 69.8% small 11-8-2-3 11 pCHR820-1 574 66.7% small 11-8-2-4 11 pCHR820-1 610 63.1% small 11-12 11 pCHR820-1 550 94.2% N.R. 11-14-1-1 11 pCHR820-1 600 97.3% large 11-14-2 11 pCHR820-1 569 97.7% large 11-15 11 pCHR820-1 565 86.7% large 11-17 11 pCHR820-1 605 98.0% large 16-2-2 16 pCHR820-1 >2000 0.0% large/abnormal 16-2-3 16 pCHR820-1 655 61.1% large/abnormal 16-2-3 16 pCHR820-1 589 48.9% large/abnormal 19-2 19 pCHR820-1 573 40.1% large 19-3-1 19 pCHR820-1 704 49.7% large 19-5-1 19 pCHR820-1 666 49.7% Large N.R. = not recorded

Pollen was also analyzed from adchromosomal T0 tobacco plants by visual analysis. The visual pollen data is summarized in Tables 46. In addition, adchromosomal T1 tobacco plants were analyzed visually and by PCR. The TI plant data is summarized in Tables 47 and 48. T1 tomato pollen, harvested from adchromosomal T0 tomato plants was also visually analyzed. 537 pollen cells were counted and 153 were fluorescent (28.5%)

TABLE 46 Visual Analysis of Adchromosomal T0 Tobacco Plants Construct Fluorescent Total Plant type Construct pollen pollen % XNN — — 0 2000 0 pNt1E mini-C TB99R7-1 79 511 15.5 pNt2A-3 mini-C TB99R10-1 289 531 54.4 pNt2D-1 mini-C TB99R10-1 323 538 60.0 pNt2H-2 mini-C TB99R10-1 251 520 48.0 pNt2E mini-C TB99R10-1 268 507 53.0 pNt2D mini-C TB99R10-1 195 508 38.0 pNt2H mini-C TB99R10-1 76 507 15.0 pNt4D-1 mini-C TB99R10-1 200 502 39.8 pNt6A mini-C pCHR488 + 18 120 15.0 TB99R1-5 pNt8B integrating pCHR488 + 479 63 650 9.7 pNt13D integrating pCHR488 + 480 188 519 36.2 pNt15B mini-C TB99R8-1 249 500 49.8 pNt15D mini-C TB99R8-1 272 506 54.0 pNt16B mini-C TB132R8-1 202 501 40.0 pNt16D mini-C TB132R8-1 277 506 55.0

TABLE 47 Visual Analysis of Adchromosomal T0 Tobacco Plants PCR scoring T0 Visual Scroing of T1 of red (+) T1 PCR scoring of Plant seedlings (self) seedlings non-Red (−) T1 Visual % (selfed) seedlings (self) Event Score counted Red Red tested positive tested positive 1 + 192 174 90% 10 6 16 0 1 + 91 79 87% 2 − 294 0 0% 2 − 393 1 0% 2 + 208 163 78% 10 10 25 0 2 + 177 126 71% 2 + 200 145 73%

TABLE 48 Visual Analysis of T1 Tobacco Seedlings Fluorescent Seedlings Plant Seedlings Counted % Fluorescent pNT 14B 0 165   0% pNT 15B 36 61 62.30%  pNT 15D 137 210 62.00%  pNT 1B(1) 79 91 86.80%  pNT 1G(2) 174 192   90% pNT 2A-1 163 208   78% pNT 2A-2 65 89 73.00%  pNT 2A-3(2) 145 200 72.5% pNT 2B-1 0 73   0% pNT 2C(2) 1 393 0.25% pNT 2C-1 0 294   0% pNT 2C-2(1) 0 204   0% pNT 2D(1) 126 177 71.1% pNT 2D(3) pNT 2E(1) 185 238 77.7% pNT 2F(1) 0 228   0% pNT 2F(2) pNT 2G(1) 14 19 73.7% pNT 2G(2) 16 24 66.7% pNT 2I(1) 0 230   0% pNT 2K(2) 156 226 69.00%  pNT 2D(2) pNT 5A 0 128 0 pNT 15A 0 78 0 pNT 19A 0 217 0

Example 14 Corn Centromere Discovery

BAC Library Construction

Two Bacterial Artificial Chromosome (BAC) libraries were constructed from corn genomic DNA. The corn genomic DNA was isolated from corn variety B73 and digested with the restriction enzymes BstYI or MboI. These enzymes were chosen because they are methylation insensitive and therefore can be used to enrich BAC libraries for centromere DNA sequences.

Probe Identification and Selection

Twenty-three groups of corn repetitive genomic or plastid sequences, including specific centromere-localized sequences, were initially compiled as candidate probes for hybridization with the BAC libraries (Table 49). These probes represented various classes of corn repetitive sequences including satellite repeats (heterochromatic/centromere-specific), retroelements, rDNA, B chromosome-specific repeats, chloroplast and mitochondrion DNA, hypermethylated or hypomethylated DNA fractions, and telomeric DNA.

TABLE 49 Maize Repetitive Sequences and Bac Library Probes GenBank Class Class Name Primers Description Reference Comment accession 1 CR CRJM-001 gypsy-type Aragon- aka CRM, AY1290008 (centromeric and 002 localized to Alcaide et al pSau3A9 retrotransposable) cen of all 1996, Jiang et (from element cereals. CentC al 1996, Zhong sorghum), and CRM co- et al 2002 CRR (from IP with CEN rice) H3 2 Cent-A CHR 15 and centromere AF082532 AF078917 16 retrotransposon, Similar includes sequence MCS1A and B 3 Huck CRJM-005 Ty3/gypsy Meyers et al (most AF050438 and 006 2001 frequent) 4 Grande CRJM-056 Ty3/gypsy Meyers et al AF050437 and 057 2001 5 Cinful CRJM-007 Ty3/gypsy Meyers et al AF049110 and 008 2001 6 Ji/Prem2 LTR-5 Ty1/copia Meyers et al from alpha CRJM-011 2001 zein seq and 012 gag CRJM- 013 and 014 7 Opie Ty1/copia Meyers et al 5′ LTR AF050453 2001 8 Tekay CRJM-009 3′ LTR AF050452 and 010 9 alpha zein AF090447 10 adh AF123535 11 bz AF448416 12 knob 180 CHR 11 and many gi|168710|gb| 12 sequences! M32521.1| MZEZMA 13 MZEHETRO CRJM-015 maize Peacock et al M35408 and 016 heterochromatic PNAS. 78, repeat (knob) 4490-4494 (1981) 14 TR-1(knob CHR 13 and Knob-specific Hsu et al 2002 3 lengths, AF071126 360) 14 multi types. Type 1 BLASTs to all 3. Cuts w/RI 15 Cent-C CHR 17 and 156 bp Ananiev et al all match AY321491 18 1998 well (Cent C27) — AF078923 158a CRJM-019 AF078922 and 020 156a 16 Cent4 CRJM-021 Chromosome 4 Page et al, AF242891 and 022 repeat 2001 homologous to B- chromosome cen repeat 17 pZmBs and S67586 B-specific Alfenito and AY173950 K5 repeats; B73 Birchler 1993; has no B Kaszas and chromosomes Birchler 1993, 1998 18 rDNA CRJM-023 maize AF013103 and 024 intergenic spacer CRJM-025 maize 5S AF273104 and 026 CRJM-027 maize 17S K0220 and 028 19 chloroplast CHHZ211 Arabidiosis and 212 CRJM-030 maize xpl X01365 and 031 rDNAs 20 mito CHHZ214 Arabidiosis and 215 CRJM-032 maize mito K01868 and 033 26S rDNA 21 hypermethylated purified complex fraction mixture 22 hypomethylated purified complex fraction mixture 23 telomere sub-telomeric U39641 U39642 repeat

Twelve probes were picked to interrogate the BAC libraries. These probes represent different groups of commonly found repetitive sequences in the corn genome. The twelve probes selected are shown in Table 49 and 50 and were: Cent-C (#15), Cent (#16), MZEHETRO (#13), TR-1 (#14), CentA (#2), CR (#1), Huck (#3), Grande (#4), 17S rDNA (#18), 5S rDNA (#18); B cen (#17), and xplmito (#19 and #20). The primers used to amplify these probes are identified in Table 49. Probes were prepared and labeled with standard molecular methods.

TABLE 50 Class Cent- 17S 5S # clones Class Properties C CentA CR Huck Grande rDNA Cent4 TR-1 MZEHETRO rDNA B cen xplmito identified I HiC LoA >=7 <7 <7 <7 <6 N/A N/A N/A N/A N/A N/A N/A 61 II HiC HiA >=7 >=6 <7 <=10 <=10 N/A N/A N/A N/A N/A N/A N/A 61 III HiCR HiC >=7 <6 >=6 <=10 <=10 N/A N/A N/A N/A N/A N/A N/A 30 IV HiA HiC >=7 >6 >=6 <=10 <=10 N/A N/A N/A N/A N/A N/A N/A 30 HiCR V HiC Hi17s >=7 >0 >0 >0 >0 >5 N/A N/A N/A N/A N/A N/A 30 VI Hi4 >0 >0 >0 >0 N/A N/A >5 N/A N/A N/A N/A N/A 17 VII HiTr1 >0 >0 N/A N/A N/A >0 N/A >6 <6 N/A N/A N/A 31 LoHet VIII LoTr1 >0 >0 N/A N/A N/A >0 N/A <5 >7 N/A N/A N/A 31 HiHet IX HiTr1 >0 >0 N/A N/A N/A >0 N/A >6 >6 N/A N/A N/A 24 HiHet Total 315 *Values represent hybridization intensities of an individual BAC to each probe on a scale of 1 to 10. Values were normalized. Library Interrogation and Data Analysis

The BAC clones from the libraries were spotted onto filters for further analysis. The filters were hybridized with each of the 12 probes to identify specific BAC clones that contain DNA from the group of sequences represented by the probe(s).

A total of 92,160 BAC clones from the two libraries (36,864 BAC clones from 2 filters from the BstYI library and 55,296 clones from 3 filters from the MboI library) were interrogated with each of the 12 probes described above sing the following hybridization conditions: 0.5×SSC 0.25% SDS at 65 degrees for 15 minutes, followed by a wash at 65 degrees for a half hour. The hybridization intensities of the BAC clones with each probe were scanned to quantitate hybridization intensity for each clone. Scores of 1 to 10 (based on the hybridization intensities, with 10 being the strongest hybridization) were imported into a relational database, for classification. The database contained a total of 24 tables, 12 from each library used in the interrogation. Each table contained the hybridization scores of each BAC clone from the BstY1 or MboI library, to one of the 12 probes. Data analysis was carried out using standard SQL (Structured Query Language) routines to find BACs that contain different groups of repetitive sequences.

Classification and Selection of BAC Clones for Mini-Chromosome Construction

BAC clones containing centromeric/heterochromatic DNA were identified by their hybridization scores to different probes. The goal was to select BAC clones that contained a diverse set of various repetitive sequences. Nine classes of centromeric BAC clones were eventually chosen to cover the broadest possible range of centromeric/heterochromatic sequences for mini-chromosome construction. Detailed descriptions of each class and probe hybridization values for each class are shown in Table 50.

Class I (HiC LoA) BAC clones had strong hybridization to probe Cent-C, but low hybridization to Cent-A, CR, Huck and Grande. Class II (HiC HiA) BAC clones had strong hybridization to both Cent-C and CentA, but low hybridization to CR. Class III (HiCR HiC) BAC clones had strong hybridization to both Cent-C and CR, but low hybridization to CentA. Class IV (HiA HiC HiCR) BAC clones had strong hybridization to Cent-C, CentA, and CR. Class V (HiC Hills) BAC clones had strong hybridization to Cent-C and 17S rDNA. Class VI (Hi4) BAC clones had strong hybridization to Cent4. Class VII (HiTri LoHet) BAC clones had strong hybridization to TR-1 but low hybridization to MZEHETRO. Class VIII (LoTr1 HiHet) BAC clones had strong hybridization to MZEHETRO but low hybridization to TR-1. Class LX (HiTri HiHet) BAC clones had strong hybridization to both TR-1 and MZEHETRO.

A number of representative clones from each class were chosen to yield a total of 315 BAC clones for further analysis by restriction digest fingerprinting.

The 315 BAC clones were fingerprinted based on restriction sites found in the centromere specific sequence(s). Fingerprinting was used to evaluate the sequence composition of the large numbers of BAC clones and to compare their similarity to each other by comparing the restriction enzyme digest fragment patterns. A sequence with a tandem repeated sequence will show a single intense band of unit repeat size when digested with a restriction enzyme that cuts within the unit repeat. Second, BAC clones with similar sequences will show similar patterns of restriction fragments in a digest.

BAC DNA was extracted from bacteria using methods familiar to those in the art. Restriction enzymes HpaII and MspI were used to digest BAC clones in Classes I through VI, and restriction enzyme NdeI was used to digest BAC clones in classes VII through IX.

Z. mays (corn) BACs ZB19 and ZB113 were deposited with the American Type Culture Collection (ATCC) P.O. Box 1549 Manassas, Va. 20108, USA on Feb. 23, 2005 and assigned Accession No. PTA-6604 and PTA-6605, respectively.

Example 15 Construction of Maize Mini-Chromosomes

The 115 BAC clones identified in Example 1 were grown up and DNA was extracted for mini-chromosome construction using NucleoBond™ Purification Kit (Clontech). To determine the molecular weight of centromere fragments in the BAC libraries, a frozen sample of bacteria harboring a BAC clone was grown in selective liquid media and the BAC DNA harvested using a standard alkaline lysis method. The recovered BAC DNA was restriction digested and resolved on an agarose gel. Centromere fragment size was determined by comparing to a molecular weight standard.

For each BAC, two types of mini-chromosomes were generated, differing only by the promoter used to express the DsRed gene. Corn ADH promoter was used to express DsRed in mini-chromosomes constructed with pCHR667 and the Arabidopsis UBQ10 promoter was used to express DsRed in mini-chromosomes constructed with pCHR758. Mini-chromosome genetic elements within the pCHR667 and pCHR758 vectors are set out in Table 51 and 52, respectively.

TABLE 51 Donor Components of pCHR667 Size Genetic Element (base pair) Location (bp) Details ADH Corn Promoter 1189  14-1202 PCR amplified maize promoter alcohol dehydrogenase 1 (ADH-1) for expression of DsRed in maize (used primers CRJM-42/43) Maize ADH Intron 579 1216-1794 PCR amplified maize ADH intron with AUG mutation for stabilization of DsRed2 gene transcript and increase protein expression level (used primers CRJM-72/73) DsRed2 + NLS 780 1817-2596 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). ADH Terminator 203 2725-2927 Amplified maize terminator using primers CRJM-46/47 Bacterial Kanamycin 817 3066-3882 Bacterial kanamycin selectable marker Rps16A terminator 489 4065-4553 Amplified from Arabidopsis thaliana 40S ribosomal protein S16 (At2g09990) for termination of NptII gene NPTII 795 4617-5411 Neomycin phosphotransferase II plant selectable marker UBQ10 intron 359 5439-5798 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression level YAT1 yeast promoter 2000 5812-7811 PCR amplified YAT1 promoter from chromosome I of Saccharomyces cerevisiae for expression of NptII in maize LoxP 34 10341-10374 and Recombination site for Cre 7829-7862 mediated recombination (Arenski et. al 1983, Abremski et. al 1984)

TABLE 52 Donor Components of pCHR758 Size Genetic Element (base pair) Location (bp) Details UBQ10 promoter 2038  14-2051 Arabidopsis thaliana polyubiquitin promoter (At4g05320) DsRed2 + NLS 780 2088-2867 Nuclear localized red fluorescent protein from Discosoma sp. (Matz, M et. al Nat Biotechnol 1999 Dec.; 17(12): 1227). Pyruvate kinase 332 3002-3333 Arabidopsis thaliana pyruvate terminator kinase terminator (At5g52920) Bacterial Kanamycin 817 3478-4294 Bacterial kanamycin selectable marker Rps16A terminator 489 4477-4965 Amplified from Arabidopsis thaliana 40S ribosomal protein S16 (At2g09990) for termination of NptII gene NPTII 795 5029-5823 Neomycin phosphotransferase II plant selectable marker UBQ10 intron 359 5851-6210 PCR amplified Arabidopsis thaliana intron from UBQ10 gene (At4g05320) for stabilization of NptII gene transcript and increase protein expression level YAT1 yeast promoter 2000 6224-8223 PCR amplified YAT1 promoter from chromosome I of Saccharomyces cerevisiae for expression of NptII in maize LoxP 34 8243-8276 & Recombination site for Cre 10755-10788 mediated recombination (Arenski et. al 1983, Abremski et. al 1984)

Corn mini-chromosomes were constructed by following a two-step procedure: Step 1: Preparation of donor DNA for retrofitting with BAC centromere vectors and Step 2: Cre-Lox Recombination-BAC and Donor DNA to generate the mini-chromosome. A total of 230 corn mini-chromosomes were constructed using this assembly process, and were subsequently tested in several different corn cell lines.

Preparation of Donor DNA for Retrofitting

Cre recombinase-mediated exchange was used to construct mini-chromosomes by combining the plant centromere fragments cloned in pBeloBAC 11 with a donor plasmid (i.e. pCHR667 or pCHR758, tables 51 & 52). The recipient BAC vector carrying the plant centromere fragment contained a loxP recombination site; the donor plasmid contained two such sites, flanking the sequences to be inserted into the recipient BAC.

Cre recombinase-mediated exchange was used to construct mini-chromosomes by combining the plant centromere fragments cloned in pBeloBAC11 with a donor plasmid (i.e. pCHR667 & pCHR758, Tables 7 and 8). The recipient BAC vector carrying the plant centromere fragment contained a loxP recombination site; the donor plasmid contained two such sites, flanking the sequences to be inserted into the recipient BAC. Mini-chromosomes were constructed using a two-step method. First, the donor plasmid was linearized to allow free contact between the two loxP site; in this step the backbone of the donor plasmid is eliminated. In the second step, the donor molecules were combined with centromere BACs and were treated with Cre recombinase, generating circular mini-chromosomes with all the components of the donor and recipient DNA. Mini-chromosomes were delivered into E. coli and selected on medium containing kanamycin and chloramphenicol. Only vectors that successfully cre recombined and contained both selectable markers survived in the medium. Mini-chromosomes were extracted from bacteria and restriction digested to verify DNA composition and calculate centromere insert size.

To determine the molecular weight of the centromere fragments in the mini-chromosomes, three bacterial colonies from each transformation event were independently grown in selective liquid media and the mini-chromosome DNA harvested using a standard alkaline lysis method. The recovered mini-chromosome was restriction digested and resolved on an agarose gel. Centromere fragment size was determined by comparing to a molecular weight standard. If variation in centromere size was noted, the mini-chromosome with the largest centromere insert was used for further experimentation.

Functional Testing of Mini-Chromosomes Using Transient Assays

Maize mini-chromosomes were tested in several corn cell lines including PCI 117, HiII, and BMS, and the procedure was optimized for antibiotic selection, cell pre-treatments, and bombardment conditions. All assays were transient and fluorescent cells were counted at several time points. Preliminary results identified several mini-chromosomes that successfully generated fluorescent cell clusters.

Example 16 Transformation and Selection of Regenerable Cells and Corn Plant Regeneration

The biolistic delivery method using wet gold particles, described in Example 2, was used to deliver the mini-chromosomes into a number of different corn tissues including suspension cells, plate-grown calli, and immature embryos. For the purpose of transient delivery or selection of stable cell culture modified with a corn mini-chromosome, suspension cells were used for delivery using wet or dry gold delivery methods. An example of such a suspension culture is the publicly available line, PC1117.

To obtain trans-chromosomal corn plants modified with corn mini-chromosomes, standard protocols for corn tissue culture and transformation are followed. Such protocols include the Maize Embryo/Callus Bombardment Protocols available at Iowa Statue University, College of Agriculture web site.

The transformation process involved the preparation of regenerable tissues such as immature embryos from corn cultivars such as HiII, pre-culture of embryos on an auxin-enriched medium, delivery of miniC's into immature embryos or embryogenic calli, selection and isolation of fluorescent cell clusters, expansion of cell clusters and formation of transchromosomal embryos, maturation and regeneration of embryos into whole plants. 

The invention claimed is:
 1. A plant comprising at least one functional, stable, and autonomous mini-chromosome, wherein the mini-chromosome comprises a plant centromere, wherein the centromere (i) comprises a polynucleotide comprising at least 5 repeated nucleotide sequences, each comprising a nucleic acid sequence having at least 95% sequence identity with SEQ ID NO:24, and (ii) confers an ability to segregate the mini-chromosome to daughter cells through cell division.
 2. The plant according to claim 1, wherein the mini-chromosome is 1000 kilobases or less in length.
 3. The plant according to claim 1, wherein the mini-chromosome comprises a site for site-specific recombination.
 4. The plant according to claim 1, wherein the mini-chromosome comprises a centromeric nucleic acid insert derived from a crop plant centromere.
 5. The plant according to claim 1, wherein the mini-chromosome comprises a centromeric nucleic acid insert that comprises artificially synthesized repeated nucleotide sequences.
 6. The plant according to claim 1, wherein the mini-chromosome is derived from a donor clone or a centromere clone and has substitutions, deletions, insertions, duplications or arrangements of one or more nucleotides in the mini-chromosome compared to the nucleotide sequence of the donor clone or centromere clone.
 7. The plant of claim 1, wherein the mini-chromosome is obtained by passage of the mini-chromosome through one or more hosts.
 8. The plant according to claim 1, wherein the mini-chromosome comprises one or more exogenous nucleic acids.
 9. The plant according to claim 8, wherein at least one exogenous nucleic acid is operably linked to a heterologous regulatory sequence functional in plant cells.
 10. The plant according to claim 1, wherein the mini-chromosome comprises an exogenous nucleic acid that confers herbicide resistance, insect resistance, disease resistance, or stress resistance on the plant.
 11. The plant according to claim 1, wherein the centromere of the mini-chromosome comprises n copies of a repeated nucleotide sequence, wherein n is less than
 1000. 12. The plant according claim 1, wherein the mini-chromosome comprises a telomere.
 13. The plant according to claim 1, wherein the mini-chromosome is circular.
 14. The plant according to claim 1, wherein the plant is a monocotyledon.
 15. The plant according to claim 1, wherein the plant is a dicotyledone.
 16. A part of the plant according to claim 1, wherein the plant part comprises the minichromosome.
 17. A meiocyte, gamete, ovule, pollen, or endosperm of the plant according to claim 1, wherein the meiocyte, gamete, ovule, pollen or endosperm comprises the minichromosome.
 18. A seed, embryo or propagule of the plant according to claim 1, wherein the seed, embryo or propagule comprises the minichromosome.
 19. A progeny of the plant according to claim 1, wherein the progeny comprises the minichromosome.
 20. The progeny of claim 19 wherein the progeny is the result of self-breeding.
 21. The progeny of claim 19 wherein the progeny is the result of cross-breeding.
 22. The progeny of claim 19 wherein the progeny is the result of apomyxis.
 23. The progeny of claim 19 wherein the progeny is the result of clonal propagation.
 24. A method of using a plant according to claim 1 to produce a food product comprising the steps of growing the plant, and harvesting or processing the plant.
 25. A method of using a plant according to claim 1, to produce a recombinant protein comprising the step of growing a plant comprising a mini-chromosome that comprises an exogenous nucleic acid encoding the recombinant protein.
 26. A method of using a plant according to claim 1 to produce a chemical product comprising the step of growing a plant comprising a mini-chromosome that comprises an exogenous nucleic acid encoding an enzyme involved in synthesis of the chemical product. 